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<a name="top"></a>MCCCS Towhee (towhee_input Version 6.2.x)</font></b></font>
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<b>Overview</b>
<ul>
This section covers the variables that are set in the towhee_input file Version 6.2.x. Each variable is listed along with its type
(logical, character, integer, or double precision). towhee_input is the main input file for Towhee and is generally the only file
that needs to be edited on a regular basis. It has a regimented style to the input. The variables are described here in the order
they appear in this file. Please look at one of the example files (available with the code package) for the precise file format.
<p></p>
Note that for each variable listed below you must include the name of the variable on the previous line. Any spaces or tabs prior to the first
non-white-space character of the variable name are ignored when the code checks for variable name matches.
<p></p>
All Towhee parameter files (including towhee_input) allow internal comments for user convenience.
Such comments are lines which begin with the '#' character; the entire line is then ignored.
<p></p>
Some variables are optional. If the variable name is not included in towhee_input it will be set to the specified default value.
Optional input file values are marked as <em>optional parameter</em>.
</ul>
<b>Bug reports and feature enhancements for 6.2.x versions</b>
<ul>
<li>6.2.19: Fixed a memory allocation bug that was causing a segmentation fault when used with 'equilibration' or 'production settings of the
<a href="#controlstyle"><b>controlstyle</b></a>. Fixed a typo in this manual page that was missing the negative sign in front of the log term
for the equation that describes how <b>kmax</b> is computed for the 'ewald_fixed_cutoff' setting of <a href="#coulombstyle"><b>coulombstyle</b></a>.
</li>
<li>6.2.18: Added missing Example files Au_Cu_Switch/towhee_coords and FENE_Hexamer/towhee_template to the distribution. Fixed a reported bug in
the ffreadsetflfile subroutine that was likely introduced in 2008. Updates to the manual pages
<a href="../towhee_pubs.html">Towhee Publications</a> and <a href="../towhee_presentations.html">Towhee Presentations</a>.
</li>
<li>6.2.17: Fixed a bug that was causing array overflows when the grand canonical ensemble was combined with more than one simulation box. Also
reworked several subroutines to replace stop statements with more graceful failures.
</li>
<li>6.2.16: Fixed a bug that was causing an infinite value of <b>kalp</b> when using a
<a href="#coulombstyle"<b>coulombstyle</b></a> value of 'ewald_fixed_cutoff' in combination with a
<a href="#numboxes"<b>numboxes</b></a> value greater than 1. Began adding support for new random number generators.
</li>
<li>6.2.15: <a href="../algorithm/cbmc.html">Configurational-bias</a> moves now have support for three membered rings and should no longer give an
error message when attempting to regrow molecules with any ring structure. The code repository has moved from cvs to svn after the old service
ceased functioning at the code home at SourceForge.
</li>
<li>6.2.14: Added a new parameter (<a href="../code/code_manual.html#MMBOND"><b>MMBOND</b></a>) to the <a href = "../code/code_manual.html">preproc.h</a>
file as the term that controls the maximum number of all of the intramolecular multi-atom interactions except the number of vibrations. This allowed
the default value of <a href="../code/code_manual.html#NNBOND"><b>NNBOND</b></a> to increase to 6 for simulation of some small molecule ions without
the dimensions of all of the other intramolecular interactions to become overly large. Made minor changes to the files that create the forcefields to
reduce spurious warning messages. Fixed some small problems as the Sodium ion and Zinc ion did not have the names specified in the
<a href ="../forcefields/dreiding.html">DREIDING</a> force field manual page.
</li>
<li>6.2.13: Several small internal changes to the code to improve compilation with certain compilers.</li>
<li>6.2.12: All <a href="../towhee_ff.html#bond_infinite_square_well">Infinite Square Well bond</a> types are now automatically set so
configurational-bias moves will use a <a href="../algorithm/cbmc.html#bond_dist_r_sq_with_bounds">R squared with bounds</a> distribution, with bounds
set to the lowest and highest bond lengths that have a non-infinite energy.
All <a href="../towhee_ff.html#angle_infinite_square_well">Infinite Square Well angle</a> types are now automatically set so configurational-bias moves
will use a <a href="../algorithm/cbmc.html#angle_dist_bounded_sine">bounded Sine distribution</a>.
Fixed the intra-box center-of-mass switch move (controlled by <a href="#pm1boxcomswitch"><b>pm1boxcomswitch</b></a>) to resolve a problem that
was occurring when using that move in combination with multiple simulation boxes.
</li>
<li>6.2.11: Resolved a minor bug that was outputting a spurious error message (introduced in 6.2.10) sometimes when performing moves on
molecules with rigid bond lengths.
</li>
<li>6.2.10: Removed the special case for the grand canonical ensemble for the default settings of the <a href="#pressurefreq"><b>pressurefreq</b></a>
parameter. Modified the treatment of rigid bond lengths and rigid bending angles in the <a href="../algorithm/cbmc.html">CBMC algorithm</a> yet again,
now treating those discrete number of allowable bond length or bending angles separately from the continuous potentials. Anyone using fixed bond
lengths or bending angles will see a shift in the <a href="../algorithm/chemicalpotential.html">chemical potentials</a>. This should also address
the noise in the chemical potential issues that were surfacing when using force fields with rigid bending angles of 180 degrees.
</li>
<li>6.2.9: Fixed an incorrect format statement in the <a href="../utils/pdb2towhee.html">pdb2towhee</a> utility addressing
<a href="https://sourceforge.net/projects/towhee/forums/forum/298241/topic/3693800">forum topic 3693800</a>.
Rewrote some faulty allocation statements related to the 'energy bias' option of the <a href="#cbmc_nb_one_generation"><b>cbmc_nb_one_generation</b></a>
variable to address
<a href="https://sourceforge.net/projects/towhee/forums/forum/298241/topic/3511354">forum topic 298241</a>.
</li>
<li>6.2.8: Removed a spurious return statement from allocate.F that was causing compilation problems on some platforms. Also began
cleaning up some of the files in the forcefield generation utility and discovered that the
<a href="../forcefields/c19eef1.html">C19eef1</a> and
<a href="../forcefields/c19sasa.html">C19sasa</a> forcefields were previously
assigning atom type ' F' instead of atom type 'Fe' for iron due to a formatting error.
</li>
<li>6.2.7: Minor changes to the manual</li>
<li>6.2.6: More internal data structure changes. Began moving some multidimensional arrays to the new globalinfo.c routines. Removed
the NMAX value from <a href="../code/code_manual.html#preproc">preproc.h</a>.
</li>
<li>6.2.5: Fixed a minor change that accidentally renamed the fitcoex utility as fitvlcc when moving it back to the Utils directory.<li>
<li>6.2.4: Added a Makefile to create all of the <a href="../utils/utility_summary.html">utility programs</a>. Moved the fitcoex utility from
the Source directory back to its original home in the Utils directory. Updated the manual pages for the utility programs.
</li>
<li>6.2.3: Some minor internal changes and updates to the manual.</li>
<li>6.2.2: Added a new configure line option (--enable-fix-GNU) to remove the double underscore problem seen when compiling on some GNU platforms.
Minor bug fixes to the <a href="../utils/fitcoex.html">fitcoex</a> manual page to better describe the required file format.
</li>
<li>6.2.1: Minor changes internal to the code to improve compilation on some platforms.</li>
<li>6.2.0: Replaced the <b>cbmc_style</b> and <b>coupled_decoupled_form</b> variables with the new
<i>optional parameter</i> <a href="#cbmc_formulation"><b>cbmc_formulation</b></a>. Made <a href="#cbmc_setting_style"><b>cbmc_setting_style</b></a>
an <i>optional parameter</i> that currently has a default of 'Martin and Frischknecht 2006'.
Changed many of the examples to use the new default settings instead of the manually specified CBMC settings.
Resolved a minor bug in engatom.F so that the declaration of dimtrials now
occurs before it is used to dimension any arrays. Resolved a problem with the angle selection involving multiple rigid angles centered on the
same atom so that cases where the mathematics does not have a solution are handled as a hard overlap instead of triggering a code failure.
This can occur when there are multiple rigid angles plus one or more flexible angles centered on the same atom.
Resolved a minor bug that ommitted the new globalinfo.c routine from the list of files required to compile the forcefield utility.
Discovered that the MM2 bond potential is not well formed and has a maximum one third of an Angstrom above the equilibrium bond length and then
heades towards negative infinity afterwards. Modified the MM2 bond potential so it now has an infinite energy for bond lengths greater than
the equilibrium bond length plus one third of an Angstrom. Modified the input utilities so now all spaces and tabs prior to the variable names are
automatically stripped before checking to see if the names listed in towhee_input match up with the expected values. There is no longer any
spacing requirement for subvariables.
</li>
</ul>
<b>towhee_input file differences from version 6.1.x</b>
<ul>
<li>Replaced the <b>cbmc_style</b> and <b>coupled_decoupled_form</b> variables with the new
<a href="#cbmc_formulation"><b>cbmc_formulation</b></a> variable.
</li>
</ul>
<b>Quick links</b>
<p>
Links to other towhee_input information pages, described elsewhere on this page:
<ul>
<li> Nonbonded potential types are described in the <a href="../potentype/towhee_input_classical_potential.html">classical_potential</a> section.</li>
<li> Information used to describe molecule-specific forcefield information is in the <a href="#inpstyle">inpstyle</a> section.</li>
<li> Various constants declared at compile-time found in <a href="../code/code_manual.html#preproc">preproc.h</a>.</li>
</ul>
</p>
<b>Variable explanations for towhee_input</b>
<ul>
<dt><a name="inputformat"><b>inputformat (character string)</b></a>
<ul>
<li>'Towhee' : reads in the input variables following the format for Towhee. This format is described in this file.</li>
<li>'LAMMPS' : reads in the input variables from the lammps_input and lammps_data files. Outputs files suitable for use with Towhee.</li>
</ul>
</dt>
<dt><a name="randomseed"><b>randomseed (integer)</b> <em>optional parameter</em></a>
<ul>
<li>The 32 bit integer seed that is used to initialize the ranlux random number generator. Must be positive. Default value is 1302002.</li>
</ul>
</dt>
<dt><a name="random_luxlevel"><b>random_luxlevel (integer)</b> <em>optional parameter</em></a>
<ul>
An integer value that defines the luxury level used by the random number generator.
See <a href="../references.html#james_1994">James 1994</a> for more information about the luxury level.
<li>0: Does not discard any pseudorandom numbers from the sequence.</li>
<li>1: Periodically discards 24 pseudorandom numbers from the sequence.</li>
<li>2: Periodically discards 73 pseudorandom numbers from the sequence.</li>
<li>3: (default value) Periodically discards 199 pseudorandom numbers from the sequence.</li>
<li>4: Periodically discards 365 pseudorandom numbers from the sequence.</li>
</ul>
</dt>
<dt><a name="random_allow_restart"><b>random_allow_restart (logical)</b> <em>optional parameter</em></a>
<ul>
<li>.TRUE. (default value) if you want to restart the random number generator from the sequence of integers in towhee_initial if possible.
This is done when the simulation is restarting from a towhee_initial file generated by Version 5.0.0 or later. If this
is not possible then Towhee will initialize the random number generator using the <a href="#randomseed"><b>randomseed</b></a>.
</li>
<li>.FALSE. if you always want to initialize the random number generator using the <a href="#randomseed"><b>randomseed</b></a>.</li>
</ul>
</dt>
<dt><a name="ensemble"><b>ensemble (character string of size 30)</b></a>
<ul>
<li> 'npt' : Isobaric-Isothermal Ensemble.
The volume moves for each simulation box are performed in an exchange with an external pressure bath set at a specified pressure.
The total number of molecules and the temperature are conserved.
See <a href="../references.html#mcdonald_1972">McDonald 1972</a> for the initial Monte Carlo molecular simulation work using the
isobaric-isothermal ensemble. Combining this ensemble with any of the two-box molecule transfer moves turns it into the NPT-Gibbs ensemble.
See <a href="../references.html#panagiotopoulos_1987">Panagiotopoulos 1987</a>,
<a href="../references.html#panagiotopoulos_et_al_1988">Panagiotopoulos <i>et al.</i> 1988</a>,
and <a href="../references.html#smit_et_al_1989">Smit <i>et al.</i> 1989</a>
for the initial Monte Carlo molecular simulation work using the Gibbs ensemble.
</li>
<li> 'nvt' : Canonical Ensemble. The total volume of the system,
The total number of each type of molecule in the system, and the temperature are conserved.
This is the prototypical ensemble for Monte Carlo molecular simulation and was first used in that context by
<a href="../references.html#metropolis_et_al_1953">Metropolis <i>et al.</i> 1953</a>.
Combining this ensemble with any of the two-box molecule transfer moves turns it into the NVT-Gibbs ensemble.
See <a href="../references.html#panagiotopoulos_1987">Panagiotopoulos 1987</a>,
<a href="../references.html#panagiotopoulos_et_al_1988">Panagiotopoulos <i>et al.</i> 1988</a>,
and <a href="../references.html#smit_et_al_1989">Smit <i>et al.</i> 1989</a>
for the initial Monte Carlo molecular simulation work using the Gibbs ensemble.
</li>
<li> 'uvt' : Grand Canonical Ensemble.
The total volume of the system is conserved. The total number of molecules in the system equilibrates with an external ideal gas bath set at
a specified chemical potential.
</li>
</ul>
</dt>
<dt><a name="temperature"><b>temperature (double precision)</b></a>
<ul>
<li> The temperature in Kelvin.</li>
</ul>
</dt>
<hr></hr>
<dt>The variable in this subsection is only included in the input file if <b>ensemble</b> is set to 'npt'</dt>
<dt><a name="pressure"><b>pressure (double precision)</b></a>
<ul>
<li> The external pressure in kPa.</li>
</ul>
</dt>
<dt>End of the subsection only included if <b>ensemble</b> is 'npt'</dt>
<hr></hr>
<dt>The variable in this subsection is only included in the input file if <b>ensemble</b> is set to 'uvt'</dt>
<dt><b>tmmc_flag (logical)</b> <em>optional parameter</em></a>
<ul>
<li>.TRUE. if you want to perform transition matrix Monte Carlo (TMMC) on a single component system in the grand canonical ensemble.
This will require other variables to be specified below.
</li>
<li>.FALSE. if you do not want to perform transition matrix Monte Carlo (TMMC). This is the default value if the parameter is not specified.</li>
</ul>
</dt>
<dt>End of the subsection only included if <b>ensemble</b> is 'uvt'</dt>
<hr></hr>
<dt><a name="nmolty"><b>nmolty (integer)</b></a>
<ul>
<li> The total number of molecule types in the simulation. This must be less then or equal to <a href="../code/code_manual.html#NTMAX">NTMAX</a>.</li>
</ul>
</dt>
<dt><a name="nmolectyp"><b>nmolectyp (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of molecules of each type (listed sequentially on a single line). For the constant N ensembles (nvt, npt) this is
the actual number of molecules in the simulation. For the constant chemical potential ensembles (uvt) this is the maximum number of molecules
allowed in the simulation.
</li>
</ul>
</dt>
<hr></hr>
<dt>The variable in this subsection is only included in the input file if <b>ensemble</b> is set to 'uvt'</dt>
<dt><a name="chempot"><b>chempot (double precision)</b></a>
<ul>
<li> The real chemical potential (this includes intramolecular portions and is identical to the CB chemical potential output by the code) for
molecules of each type (listed sequentially on a single line). The units are in Kelvin (identical to the output CB chemical potential).
</li>
</ul>
</dt>
<dt>End of the subsection only included if <b>ensemble</b> is 'uvt'</dt>
<hr></hr>
<dt><a name="numboxes"><b>numboxes (integer)</b></a>
<ul>
<li> The number of simulation boxes in the system. This value must be less than or equal to <a href="../code/code_manual.html#MAXBOX">MAXBOX</a>
Note that many of the variables below depend upon <b>numboxes</b> as information is required based on the number of simulation boxes
(such as box lengths) and some Monte Carlo moves are only valid for multiple box ensembles.
</li>
</ul>
</dt>
<dt><a name="stepstyle"><b>stepstyle (character string of length 10)</b></a>
<ul>
<li> 'cycles': Run a Monte Carlo simulation for <b>nstep</b> Monte Carlo cycles.
A cycle is equal to <b>N</b> Monte Carlo moves, where <b>N</b> is the number of molecules in the system.
</li>
<li> 'moves': Run a Monte Carlo simulation for <b>nstep</b> Monte Carlo moves.</li>
</ul>
</dt>
<dt><a name="nstep"><b>nstep (integer)</b></a>
<ul>
<li> The number of Monte Carlo steps to perform where each step is either a full Monte Carlo
cycles (if <b>stepstyle</b> is 'cycles') or a single move (if <b>stepstyle</b> is 'moves')
</li>
</ul>
</dt>
<dt><a name="controlstyle"><b>controlstyle (character*20)</b> <em>optional parameter</em></a>
<ul>
<li>'equilibration': designed for use when you are first setting up a simulation and still need to rapidly equilibrate all of the maximum update
values. This option sets the following parameters based upon the value of <b>nstep</b>.
<ul>
<li><b>printfreq</b> = <b>nstep</b>/10</li>
<li><b>blocksize</b> = <b>nstep</b>/5</li>
<li><b>moviefreq</b> = <b>nstep</b>/5</li>
<li><b>backupfreq</b> = <b>nstep</b>/5</li>
<li><b>runoutput</b> = 'full'</li>
<li><b>pdb_output_freq</b> = <b>nstep</b>/5</li>
<li><b>loutdft</b> = .FALSE.</li>
<li><b>loutlammps</b> = .FALSE.</li>
<li><b>loutdlpoly</b> = .FALSE.</li>
<li><b>louthist</b> = .FALSE.</li>
<li><b>pressurefreq</b> = 10</li>
<li><b>trmaxdispfreq</b> = <b>nstep</b>/100</li>
<li><b>volmaxdispfreq</b> = <b>nstep</b>/100</li>
</ul>
</li>
<li>'production': designed for use during production runs. This option sets the following parameters based upon the value of <b>nstep</b>.
<ul>
<li><b>printfreq</b> = <b>nstep</b>/10</li>
<li><b>blocksize</b> = <b>nstep</b>/5</li>
<li><b>moviefreq</b> = <b>nstep</b>/20</li>
<li><b>backupfreq</b> = <b>nstep</b>/5</li>
<li><b>runoutput</b> = 'full'</li>
<li><b>pdb_output_freq</b> = <b>nstep</b>/5</li>
<li><b>loutdft</b> = .FALSE.</li>
<li><b>loutlammps</b> = .FALSE.</li>
<li><b>loutdlpoly</b> = .FALSE.</li>
<li><b>louthist</b> = .FALSE.</li>
<li><b>pressurefreq</b> = 10</li>
<li><b>trmaxdispfreq</b> = <b>nstep</b>/10</li>
<li><b>volmaxdispfreq</b> = <b>nstep</b>/10</li>
</ul>
</li>
<li>'manual': This is the default setting if no other value of <b>controlstyle</b> is specified. When using this option you must also
include the following variables
<ul>
<dt><a name="printfreq"><b>printfreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for outputting information about the system to standard output (fortran unit 6). The information is the number of Monte
Carlo steps performed thus far during the run, the total energy in each box, the x-box length of each box, the pressure of each
box, and the number of molecules of each type in each box. If printfreq = 0, or if it is not specified, there will be no output.
</li>
</ul>
</dt>
<hr></hr>
<dt>Variables in this subsection only need to be specified if <b>tmmc_flag</b> is .TRUE..</dt>
<dt><b>n_tmmc_min (integer) </b><i>optional</i>
<ul>
<li>Minimum number of molecules allowed in the simulation box. By default, this is set to 0. Specifying a non-zero value is useful when sampling
specific molecule number ranges. The maximum number is set to <b>nmolty</b>.
</li>
</ul>
</dt>
<dt><b>weight_freq (integer)</b>
<ul>
<li>The step frequency for updating the biasing function for transition-matrix Monte Carlo.</li>
</ul>
</dt>
<dt><b>c_matrix_freq (integer)</b>
<ul>
<li>The step frequency for writing to file the collection matrix for TMMC. A new file indicating the step number will be created.</li>
</ul>
</dt>
<dt><b>run_name (character)</b>
<ul>
<li>File prefix for TMMC output. The current estimate of the natural logarithm of the particle number probability distribution is written to a
file "run_name.tmmc_weights.dat" every time the biasing function is updated. Collection matrix info is written to
a file "run_name.c.stepnumber.dat". Accumulated semigrand potential energies are written to a file "run_name.vsg.stepnumber".
This information is useful if one is interested in the average potential energy as a function density.
</li>
</ul>
</dt>
<dt><b>in_c_flag (logical)</b> <i>optional parameter</i>
<ul>
<li>By default, set to .FALSE. Set this variable to .TRUE. if an initial collection matrix is to be used to initiate the TMMC simulation. In the
future, this will be modified so that either a collection matrix or biasing function can be read in. This option can be used to for continuing
a TMMC simulation.
</li>
</ul>
</dt>
<dt><b>in_cfile (character)</b> <i>optional parameter</i>
<ul>
<li>Name of the collection matrix input file to be read in. Only needed if <b>in_c_flag</b> is .TRUE..</li>
</ul>
</dt>
<dt>End of variables subsection when <b>tmmc_flag</b> is .TRUE..</dt>
<hr></hr>
<dt><a name="blocksize"><b>blocksize (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The size of the blocks for computing block averages. If you want this to be meaningful then blocksize should divide cleanly into nstep.
The quantities that are averaged (in each simulation box) are the specific density, the pressure, all of the energy terms, the chemical
potential of each molecule type, number density of each molecule type, and the mole fractions. If blocksize=0, or if it is not
specified, no block output takes place.
</li>
</ul>
</dt>
<dt><a name="moviefreq"><b>moviefreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for outputting the system conformations to the towhee_movie file. This file is analyzed after the run using
the analyze_movie.F routine to compute a variety of distribution functions. This file can get pretty big if you output frequently
so be careful if you have a limited amount of hard disk space available. If moviefreq=0, or if it is not specified, this file is not written.
</li>
</ul>
</dt>
<dt><a name="backupfreq"><b>backupfreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for writing a file named towhee_backup that is suitable for use as a restart file. It overwrites
the previous version of towhee_backup each time so it does not take up much space. Typically I set backupfreq so that I get around 10 backups
during a run. For more information about restart files look at the manual entries for towhee_initial, towhee_backup, and towhee_final.
If backupfreq=0, or if it is not specified, this file is not written.
</li>
</ul>
</dt>
<dt><a name="restartfreq"><b>restartfreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for writing a file named towhee_restart_NNN that is suitable for use as a restart file,
where NNN represents the step number at which this file is written. This file is identical to towhee_backup (see <b>backupfreq</b> above),
except that it is not overwritten by subsequent restart files, and allows for restarts from multiple points along a run.
If restartfreq=0, or if it is not specified, this file is not written.
</li>
</ul>
</dt>
<dt><a name="runoutput"><b>runoutput (character*20)</b></a>
<ul>
<li>'full': if you want information about the individual blocks of the block averages and information about the maximum displacement updates.</li>
<li>'blocks': if you want information about the individual blocks of the block averages and don't want information about the maximum
displacement updates.
</li>
<li>'updates': if you don't want information about the individual blocks of the block averages and do want information about the maximum
displacement updates.
</li>
<li>'none': if you don't want information about the individual blocks of the block averages or information about the maximum displacement updates.
</li>
</ul>
</dt>
<dt><a name="pdb_output_freq"><b>pdb_output_freq (integer)</b> <em>optional parameter</em></a>
<ul>
<li>The step frequency for outputting a snapshot of the simulation to a pdb file named box_xx_step_yyyyyyyyyyyyyy.pdb where xx is the box number
converted into a 2 character string and yyyyyyyyyyyyyy is the step number converted into a 14 character string.
If you do not wish to output any pdb files then you can set <b>pdb_output_freq</b> to 0 to disable this feature.
</li>
</ul>
</dt>
<dt><a name="loutdft"><b>loutdft (logical)</b> <em>optional parameter</em></a>
<ul>
<li> .TRUE. if you wish to output files for use with the Tramonto classical density functional theory code. This outputs dft_surfaces.dat
and dft_decode.dat. See the <a href="http://software.sandia.gov/DFTfluids/">Tramonto manual</a> for information about these files.
</li>
<li> .FALSE. (default value) if you do not want to output dft files.</li>
</ul>
</dt>
<dt><a name="loutlammps"><b>loutlammps (logical)</b> <em>optional parameter</em></a>
<ul>
<li> .TRUE. if you wish to output files for use with the LAMMPS massively parallel molecular dynamics code. This outputs lammps_input and
lammps_data# where the number is each of the simulation box numbers. See the <a href="http://lammps.sandia.gov/">LAMMPS manual</a>
for more information on how to read in these files.
</li>
<li> .FALSE. (default value) if you do not want to output LAMMPS files.</li>
</ul>
</dt>
<dt><a name="loutdlpoly"><b>loutdlpoly (logical)</b> <em>optional parameter</em></a>
<ul>
<li> .TRUE. if you wish to output files for use with the DL_POLY molecular dynamics code. This outputs CONFIG# and
FIELD# where the number is each of the simulation box numbers.
See the <a href="http://www.cse.clrc.ac.uk/msi/software/DL_POLY/">DL_POLY manual</a> for more information about these files.
</li>
<li> .FALSE. (default value) if you do not want to output DL_POLY files.</li>
</ul>
</dt>
<hr></hr>
<dt>The variables in this subsection are only included if <b>ensemble</b> is 'uvt'</dt>
<dt><a name="louthist"><b>louthist (logical)</b> <em>optional parameter</em></a>
<ul>
<li>.FALSE. (default value) will not output files for histogram reweighting. No additional variables are required for this setting.</li>
<li>.TRUE. will output files used for histogram reweighting. When set to this value you must also include the following additional
variables
<ul>
<dt><a name="hist_label"><b>hist_label (integer)</b></a>
<ul>
<li>An integer that is turned into a character string that creates the X portion of the named towhee_hisXY.dat file that is used to
output information for histogram reweighting.
</li>
</ul>
</dt>
<dt><a name="hist_suffix"><b>hist_suffix (character*1)</b></a>
<ul>
<li>A single character that creates the Y portion of the named towhee_hisXY.dat file that is used to output information for histogram
reweighting.
</li>
</ul>
</dt>
<dt><a name="hist_nequil"><b>hist_nequil (integer)</b></a>
<ul>
<li>The number of steps (cycles or moves) that are disregarded for the purposes of outputting histogram information. Set to 0 if you wish to
use all of the steps for computing the histogram, and set to a positive number in order to discard those initial steps from the histogram.
</li>
</ul>
</dt>
<dt><a name="histcalcfreq"><b>histcalcfreq (integer)</b></a>
<ul>
<li>The step frequency for computing the information needed for histogram reweighting.</li>
</ul>
</dt>
<dt><a name="histdumpfreq"><b>histdumpfreq (integer)</b></a>
<ul>
<li>The step frequency for outputting the information needed for histogram reweighting to the various towhee_histogram files. The ratio of
<b>histdumpfreq</b>/<b>histcalcfreq</b> must be less than <a href="../code/code_manual.html#NDUMPHIST">NDUMPHIST</a>.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt>End of the subsection only included if <b>ensemble</b> is 'uvt'</dt>
<hr></hr>
<dt><a name="pressurefreq"><b>pressurefreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for computing the pressure via the pressure virial (for continuous potentials) or the radial pressure
(for discontinuous potentials) in each simulation box. Be aware that computing the pressure is a relatively expensive task (especially for large
systems). If you do not wish to compute the pressure using these methods you can set the <b>pressurefreq</b> to zero to disable this calculation.
If the parameter is not specified, the default value is 0.
</li>
</ul>
</dt>
<dt><a name="trmaxdispfreq"><b>trmaxdispfreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for updating the maximum translational (atom and center-of-mass) and rotational displacements. They are adjusted to try and
achieve the target acceptance rates (see <b>tatraa</b>, <b>tatrac</b>, and <b>tarot</b>). It is a good idea to do this fairly frequently at the
start of the simulation (every step or every 10 steps) in order to get good values for the maximum displacements. Once the acceptance rates are
near their desired values then reset <b>trmaxdispfreq</b> to do 10 updates during a run. If <b>trmaxdispfreq</b> is 0, or if it is not specified,
no updates take place.
</li>
</ul>
</dt>
<dt><a name="volmaxdispfreq"><b>volmaxdispfreq (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The step frequency for updating the maximum volume displacements. They are adjusted to try and achieve the target acceptance rates
(see <b>tavol</b>). It is a good idea to do this fairly frequently at the start of the simulation (every few steps) in order to get good values
for the maximum displacements. Once the acceptance rates are near their desired values I typically set <b>volmaxdisp</b> to do 10 updates during
a run. If <b>volmaxdispfreq</b> is set to 0, or if it is not specified, no such updates take place.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="chempotperstep"><b>chempotperstep (integer)</b> <em>optional parameter</em></a>
<ul>
<li> The number of additional trial insertions to perform in each box for at the end of every Monte Carlo step (listed sequentially for each molecule
type on a single line). This allows the measurement of chemical potential in ensembles that do not have an insertion and deletion move (such as
canonical and isobaric-isothermal). Default value is 0 for all molecule types
</li>
</ul>
</dt>
<dt><a name="potentialstyle"><b>potentialstyle</b></a>
<ul>
<li>'internal': uses energy routines internal to the Towhee software package to describe the energies between atoms.
When using this option you must include the following variables.
<ul>
<dt><a name="ffnumber"><b>ffnumber (integer)</b></a>
<ul>
<li> 1 or more: reads the force field information from this number of file(s) listed in the <b>ff_filename</b>.</li>
</ul>
</dt>
<dt><a name="ff_filename"><b>ff_filename (formatted character*70) [one line for each force field]</b></a>
<ul>
<li>A list of the filenames (one per line) that contain the force field information. On most systems you can just list this directory and then
end the line. However, if you have trouble then adding sufficient blank spaces to the end of the line to get up to 70 characters could
resolve your problem.
</li>
</ul>
</dt>
<dt><a name="classical_potential"><b>classical_potential (character*30)</b></a>
<ul>
The setting for this variable controls the nonbonded potential type. Depending on the setting there are a number of other variables that are
also required.
Please see the <a href="../potentype/towhee_input_classical_potential.html">classical_potential</a> web page for more information.
</ul>
</dt>
<dt><a name="electrostatic_form"><b>electrostatic_form (character*50)</b></a>
<ul>
<li>'none' : no electrostatic potential</li>
<li>'coulomb' : use Coulomb's law for the electrostatic potential. This option requires the following variables.
<ul>
<dt><a name="coulombstyle"><b>coulombstyle (character*20)</b></a>
<ul>
<li>'ewald_fixed_kmax' if you want to use point charges with an Ewald sum that utilizes a constant number of inverse space vectors
(<b>kmax</b>) and a variable electrostatic cutoff (<b>rcelect</b>) equal to half the current box length. When using this option you
also need the following variables.
<ul>
<dt><a name="kalp"><b>kalp (double precision)</b></a>
<ul>
<li> Value used in the Ewald sum to compute alpha. The actual Ewald sum alpha term is equal to <b>kalp</b> divided by the shortest
box length. The recommended value for <b>kalp</b> is 5.6.
</li>
</ul>
</dt>
<dt><a name="kmax"><b>kmax (integer)</b></a>
<ul>
<li> Maximum number of inverse space vectors to use in any dimension for the Ewald sum. Recommended value of this parameter is 5.
If you want to set this to a larger value to may have to increase <a href="../code/code_manual.html#VECTORMAX">VECTORMAX</a>.
</li>
</ul>
</dt>
<dt><a name="dielect"><b>dielect (double precision)</b></a>
<ul>
<li> The dielectric constant used when computing coulombic interactions. Generally this should be set to 1.0 as the solvated system
will act as the screening that the dielectric constant is intended to represent. If you are performing a simulation without any
solvent (for example a protein without the water) you might want to set this value to the dielectric constant of the missing solvent.
</li>
</ul>
</dt>
</ul>
</li>
<li>'ewald_fixed_cutoff' if you want to use point charges with an Ewald sum that utilizes a constant electrostatic cutoff (<b>rcelect</b>)
and adjusts the number of inverse space vectors (<b>kmax</b>) according to the following heuristic.
<dt>alpha = ( 1.35 - 0.15 log[<b>ewald_prec</b>]) / <b>rcelect</b></dt>
<dt>kmax = ( alpha * Max[box length] / π) * (-log[<b>ewald_prec</b>])<sup>0.5</sup></dt>
When using this option you will also need to list the following variables.
<ul>
<dt><a name="ewald_prec"><b>ewald_prec (double precision)</b></a>
<ul>
<li> Controls the precision of the Ewald summation technique. The smaller the value, the better the results (and the more expensive the
simulation). The recommended value of 1d-4 is generally adequate, while a value of 1d-5 is very good (but more expensive).
</li>
</ul>
</dt>
<dt><a name="rcelect"><b>rcelect (double precision)</b></a>
<ul>
<li>The cutoff for electrostatic interactions computed in the "real space" portion of the Ewald sum. Decreasing this value means less
work in the "real space", but correspondingly more work in the "inverse space". Setting this equal to the general nonbonded cutoff
(see <b>rcut</b> in <a href="../potentype/towhee_input_classical_potential.html">classical_potential</a>) is recommended.
</li>
</ul>
</dt>
<dt><a name="dielect"><b>dielect (double precision)</b></a>
<ul>
<li> The dielectric constant used when computing coulombic interactions. Generally this should be set to 1.0 as the solvated system
acts as the screening that the dielectric constant is intended to represent. If you are performing a simulation without any solvent
(for example a protein without the water) you could set this value to the dielectric constant of the missing solvent.
</li>
</ul>
</dt>
</ul>
</li>
<li>'minimum image' uses the minimum image convention to compute the coulombic interactions between all pairs of atoms in a system. Please
note that this option is implemented mainly to compute single-molecule energies for test systems and is not suggested for routine use in
periodic systems. For a discussion of the perils of using cut-off methods for Coulombic interactions please see
<a href="../references.html#hummer_et_al_1997">Hummer <i>et al.</i> 1997</a>. When using this option you must list the following variable.
<ul>
<dt><a name="dielect"><b>dielect (double precision)</b></a>
<ul>
<li> The dielectric constant used when computing coulombic interactions. Generally this should be set to 1.0 as the solvated system
acts as the screening that the dielectric constant is intended to represent. If you are performing a simulation without any solvent
(for example a protein without the water) you could set this value to the dielectric constant of the missing solvent.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="max_bond_length"><b>max_bond_length (double precision)</b> <em>optional parameter</em></a>
<ul>
<li>The maximum allowed value for any bond length in the simulation. Any bond lengths greater than this value are given an infinite energy
regardless of the actual form of the bond length potential. This value is also used in order to normalize the bond length distribution in a
configurational-bias move and therefore will affect the measured chemical potential. If no value is specified for this optional parameter then
the default value of 3.0 is used instead.
</li>
</ul>
</dt>
<dt><a name="nfield"><b>nfield (integer)</b> <em>optional parameter</em></a>
<ul>
The number of external fields to apply in the simulation. These fields can take on a variety of forms, but are always applied relative to a
plane in one of the simulation boxes. Typical uses are for simulating the effect of a rigid surface without having to treat the surface atoms
explicitly. If this value is not specified then it is set to the default value of 0.
For nonzero values of <b>nfield</b>, the following variables are required for for each field.
<dt><a name="fieldtype"><b>fieldtype (character*20)</b></a>
<ul>
<li>'Hard Ball': Places a hard ball of a specified diameter at a particular location in one of the boxes.
This ball interacts with each atom in the simulation and excludes all atom centers from its radius.
When using this option you must also specify the following variables.
<ul>
<dt><a name="hrbbox"><b>hrbbox (integer)</b></a>
<ul>
<li>The number of the simulation box which contains this hard ball. Must range from 1 to <b>numboxes</b>.</li>
</ul>
</dt>
<dt><a name="hrbpos"><b>hrbpos (double precision)</b></a>
<ul>
<li> Position of the center of the hard ball. Must be between 0.0 and the box length of each of the 3 axes. All three coordinates
are listed on the same line.
</li>
</ul>
</dt>
<dt><a name="hrbrad"><b>hrbrad (double precision)</b></a>
<ul>
<li> Radius of the hard ball. The ball is felt through the periodic boundaries.</li>
</ul>
</dt>
<dt><a name="hrbfac"><b>hrbfac (double precision)</b></a>
<ul>
<li> Factor used to rescale the size of the hard ball. A value of 1.0 will use the <b>hrbrad</b> value without any adjustment.
This factor is multiplied by the <b>hrbrad</b> value to compute the true radius of the hard ball.
</li>
</ul>
</dt>
<dt><a name="hrb_energy_type"><b>hrb_energy_type (character*11)</b></a>
<ul>
<li>'infinite': for a hard overlap with the ball of infinite energy</li>
<li>'finite': for a specfic finite penalty for each atom that is inside of the hard ball. When using this option you also need the
following variable.
<ul>
<dt><a name="hrb_ball_energy"><b>hrb_ball_energy (double precision)</b></a>
<ul>
<li>The energy penalty in units of K/k<sub>B</sub> for each atom that overlaps with a hard ball.</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
<li>'Hard Wall': Places a hard wall of a specified diameter in one of the boxes. This wall interacts with each atom in the simulation. When
using this option you must also specify the following variables.
<ul>
<dt><a name="hrdbox"><b>hrdbox (integer)</b></a>
<ul>
<li>The number of the simulation box which contains this hard wall. Must range from 1 to <b>numboxes</b>.</li>
</ul>
</dt>
<dt><a name="hrdxyz"><b>hrdxyz (character*1)</b></a>
<ul>
<li>'x': hard wall is perpendicular to the x-axis (in the yz plane)</li>
<li>'y': hard wall is perpendicular to the y-axis (in the xz plane)</li>
<li>'z': hard wall is perpendicular to the z-axis (in the xy plane)</li>
</ul>
</dt>
<dt><a name="hrdcen"><b>hrdcen (double precision)</b></a>
<ul>
<li> Position of the center of the hard wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.</li>
</ul>
</dt>
<dt><a name="hrdrad"><b>hrdrad (double precision)</b></a>
<ul>
<li> Radius of the hard wall. The wall is felt through the periodic boundaries.</li>
</ul>
</dt>
<dt><a name="hrd_repulsion_style"><b>hrd_repulsion_style (character*11)</b></a>
<ul>
<li>'centers': the center of each atom in the system is the portion that interacts with the hard wall region. In other words, the hard
wall interacts with the atoms as if they were point particles.
</li>
<li>'hard radii': the atoms are considered to have a radius that is determined by their nonbonded parameters. The distance between the
surface of the hard wall and the closest approach of the atomic radius is used to determine the interactions between the wall and the
atoms.
This option is not currently supported for all choices of the <b>classical_potential</b>.
</li>
</ul>
</dt>
<dt><a name="hrd_energy_type"><b>hrd_energy_type (character*11)</b></a>
<ul>
<li>'infinite': any molecule inside of the hard wall has an infinite energy (hard overlap).</li>
<li>'finite': any molecule inside of the hard wall has a finite energy that is specified by the <b>hrd_wall_energy</b> variable.
If you use this option you must include the following variable
<ul>
<dt><a name="hrd_wall_energy"><b>hrd_wall_energy (double precision)</b></a>
<ul>
<li>The energy given to any atom that is inside of the hard wall (in Kelvin). This option is designed to enable equilibrium of a hard
wall system as this provides an incentive for molecules to leave the hard wall area without causing a simulation ending overlap.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
<li>'Harmonic Attractor': Uses a harmonic potential to root certain atoms to a defined point or their initial positions.
<ul>
<dt><a name="hafbox"><b>hafbox (integer)</b></a>
<ul>
<li>The number of the simulation box in which this harmonic attractor is employed. Must range from 1 to numboxes.</li>
</ul>
</dt>
<dt><a name="hafk"><b>hafk (double precision)</b></a>
<ul>
<li>The force constant for the harmonic potential.</li>
</ul>
</dt>
<dt><a name="hafentries"><b>hafentries (integer)</b></a>
<ul>
<li>The number of types or elements to which this field is applied. </li>
</ul>
</dt>
<dt><a name="hafrefpos"><b>hafrefpos (character*7)</b></a>
<ul>
<li>'Global': Uses a global set of coordinates for each atom. When using this option you also need to include the following variable.
<ul>
<dt><b>hafglobxyz (double precision array)</b></a>
<ul>
<li>The x,y, and z coordinates of the global position. This should be entered all on the same line just separated by spaces.</li>
</ul>
</dt>
</ul>
</li>
<li> 'Initial': Uses the initial coordinates of each atom.</li>
</ul>
</dt>
<dt><a name="hafkey"><b>hafkey (character*7)</b></a>
<ul>
<li>'Element': Allows the user to chose to apply this field to a specific group of atoms which are all the same type of element. The
following variables must be included for each entry.
<ul>
<dt><a name="hafmolec"><b>hafmolec (integer)</b></a>
<ul>
<li>The field is applied to the element of choice in this molecule number.</li>
</ul>
</dt>
<dt><a name="hafelement"><b>hafelement (character*2)</b></a>
<ul>
<li>The element type to which apply this field. </li>
</ul>
</dt>
</ul>
</li>
<li>'FFtype': Allows the user to chose to apply this field to a specific group of atoms which are all the same nonbond type. The
following variables must be included for each entry.
<ul>
<dt><a name="hafmolec"><b>hafmolec (integer)</b></a>
<ul>
<li>The field is applied to the element of choice in this molecule number.</li>
</ul>
</dt>
<dt><a name="hafname"><b>hafname (character*10)</b></a>
<ul>
<li>The nonbond type to which apply this field. </li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
<li>'Hooper Umbrella': Places a Hooper Umbrella field (see <a href="../references.html#hooper_et_al_2000">Hooper <i>et al.</i> 2000</a>) in a
simulation box. This is a 4th power energy function based on displacement along a single axis.
<dt>v(d) = umba * [ (d - umbcenter) / umbcenter ]</dt>
With this option you must also specify the following variables.
<ul>
<dt><a name="umbbox"><b>umbbox (integer)</b></a>
<ul>
<li>The number of the simulation box which contains this Umbrella field. Must range from 1 to numboxes.</li>
</ul>
</dt>
<dt><a name="umbxyz"><b>umbxyz (character*1)</b></a>
<ul>
<li>'x': Field is perpendicular to the x-axis (in the yz plane)</li>
<li>'y': Field is perpendicular to the y-axis (in the xz plane)</li>
<li>'z': Field is perpendicular to the z-axis (in the xy plane)</li>
</ul>
</dt>
<dt><a name="umbcenter"><b>umbcenter (double precision)</b></a>
<ul>
<li>The zero energy point of the field, listed as a distance in Angstroms along the axis specified in <b>umbxyz</b></li>
</ul>
</dt>
<dt><a name="umba"><b>umba (double precision)</b></a>
<ul>
<li>The energy constant in units of K/k<sub>B</sub>.</li>
</ul>
</dt>
</ul>
</li>
<li>'LJ 9-3 Wall': Places a 9-3 Lennard-Jones wall in one of the simulation boxes. The wall potential has the following functional form.
<dt>v(d) = [ 2/3 π ε<sub>wf</sub> σ<sub>wf</sub><sup>3</sup> ρ<sub>wall</sub> ]
* [ 2/15 (σ<sub>wf</sub>/d)<sup>9</sup> - (σ<sub>wf</sub>/d)<sup>3</sup> ]
</dt>
With this option you must also specify the following variables.
<ul>
<dt><a name="ljfbox"><b>ljfbox (integer)</b></a>
<ul>
<li> The number of the simulation box which contains this Lennard-Jones wall. Must range from 1 to numboxes.</li>
</ul>
</dt>
<dt><a name="ljfxyz"><b>ljfxyz (character*1)</b></a>
<ul>
<li>'x': Lennard-Jones wall is perpendicular to the x-axis (in the yz plane)</li>
<li>'y': Lennard-Jones wall is perpendicular to the y-axis (in the xz plane)</li>
<li>'z': Lennard-Jones wall is perpendicular to the z-axis (in the xy plane)</li>
</ul>
</dt>
<dt><a name="ljfcen"><b>ljfcen (double precision)</b></a>
<ul>
<li> Position of the center of the Lennard-Jones wall. Must be between 0.0 and the box length of the axis that is perpendicular to the
wall.
</li>
</ul>
</dt>
<dt><a name="ljfdir"><b>ljfdir (integer)</b></a>
<ul>
<li> -1: Atoms only interact with the "left" face of this wall. This does not extend through the periodic boundary.</li>
<li> 1: Atoms only interact with the "right" face of this wall. This does not extend through the periodic boundary.</li>
</ul>
</dt>
<dt><a name="ljfcut"><b>ljfcut (double precision)</b></a>
<ul>
<li> The distance beyond which the wall-atom interactions are not computed and assumed to be zero.</li>
</ul>
</dt>
<dt><a name="ljfshift"><b>ljfshift (logical)</b></a>
<ul>
<li>T: if you want to shift the lj wall potential to be zero at the cutoff.</li>
<li>F: if you do not want to shift the potential.</li>
</ul>
</dt>
<dt><a name="ljfrho"><b>ljfrho (double precision)</b></a>
<ul>
<li>The number density of atoms in the integrated wall potential (units of atoms per cubic Angstrom).</li>
</ul>
</dt>
<dt><a name="ljfntypes"><b>ljfntypes (integer)</b></a>
<ul>
<li>The number of atom types in the system that interact with the wall. Any atom type not listed here will have zero interaction with
the wall. For each value of <b>ljfntypes</b> you must list the following variables.
<ul>
<dt><a name="ljfname"><b>ljfname (character*6)</b></a>
<ul>
<li> The name of the atom. This must match up with the atom names listed in the <b>inpstyle</b>=2 portion of each molecule that is
interacting with this wall. If you are not using that <b>inpstyle</b> this will still work except you will need to know the atom
names in the appropriate towhee_ff_* files.
</li>
</ul>
</dt>
<dt><a name="ljfsig"><b>ljfsig (double precision)</b></a>
<ul>
<li> σ parameter for the interaction between this atom and the wall atoms. Units are Angstroms.</li>
</ul>
</dt>
<dt><a name="ljfeps"><b>ljfeps (double precision)</b></a>
<ul>
<li> ε parameter for the interaction between this atom and the wall atoms. Units are K/k<sub>B</sub>.</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
<li>'Steele Wall': Places a 10-4 Lennard-Jones wall in one of the simulation boxes. The wall potential has the following functional form.
<dt>v(z) = ε<sub>w</sub> [ 2/5 (σ<sub>sf</sub>/z)<sup>10</sup> - (σ<sub>sf</sub>/z)<sup>4</sup>
- σ<sub>sf</sub><sup>4</sup> / [ 3 Δ ( z + 0.61 Δ )<sup>3</sup> ] ]
</dt>
where
<dt>ε<sub>w</sub> = 2 π ε<sub>sf</sub> ρ<sub>s</sub> σ<sub>sf</sub><sup>2</sup> Δ</dt>
This potential is attributed to <a href="../references.html#steele_1973">Steele 1973</a>, but I found that reference a bit confusing so I
implemented the equations as presented in <a href="../references.html#lastoskie_et_al_1993">Lastoskie <i>et al.</i> 1993</a> and the variable
names here follow the notation in that paper.
<dt>With this option you must also specify the following variables.</dt>
<ul>
<dt><a name="steele box"><b>steele box (integer)</b></a>
<ul>
<li> The number of the simulation box which contains this Steele wall. Must range from 1 to numboxes.</li>
</ul>
</dt>
<dt><a name="steele xyz"><b>steele xyz (character*1)</b></a>
<ul>
<li>'x': wall is perpendicular to the x-axis (in the yz plane)</li>
<li>'y': wall is perpendicular to the y-axis (in the xz plane)</li>
<li>'z': wall is perpendicular to the z-axis (in the xy plane)</li>
</ul>
</dt>
<dt><a name="steele surface"><b>steele surface (double precision)</b></a>
<ul>
<li> Position of the surface of the wall. Must be between 0.0 and the box length of the axis that is perpendicular to the wall.</li>
</ul>
</dt>
<dt><a name="steele dir"><b>steele dir (integer)</b></a>
<ul>
<li> -1: Atoms only interact with the "left/bottom" face of this wall. This does not extend through the periodic boundary.</li>
<li> 1: Atoms only interact with the "right/top" face of this wall. This does not extend through the periodic boundary.</li>
</ul>
</dt>
<dt><a name="steele cutoff"><b>steele cutoff (double precision)</b></a>
<ul>
<li> The distance beyond which the wall-atom interactions are not computed and assumed to be zero.</li>
</ul>
</dt>
<dt><a name="steele shift"><b>steele shift (logical)</b></a>
<ul>
<li>T: if you want to shift the wall potential to be zero at the cutoff.</li>
<li>F: if you do not want to shift the potential.</li>
</ul>
</dt>
<dt><a name="steele delta"><b>steele delta (double precision)</b></a>
<ul>
<li>Δ parameter for the spacing between the layers in the solid. Units are in Angstroms.</li>
</ul>
</dt>
<dt><a name="steele rho_s"><b>steele rho_s (double precision)</b></a>
<ul>
<li>ρ<sub>s</sub> parameter for the density of the atom in the solid. Units are in atoms per cubic Angstrom.</li>
</ul>
</dt>
<dt><a name="steele ntype"><b>steele ntype (integer)</b></a>
<ul>
<li>The number of atom types in the system that interact with the wall. Any atom type not listed here will have zero interaction with the
wall. For each type you must list the following variables.
<ul>
<dt><a name="steele name"><b>steele name (character*6)</b></a>
<ul>
<li> The name of the atom. This must match up with the atom names listed in the <b>inpstyle</b>=2 portion of each molecule that is
interacting with this wall. If you are not using that <b>inpstyle</b> this will still work except you will need to know the atom
names in the appropriate towhee_ff_whatever files.
</li>
</ul>
</dt>
<dt><a name="sigma_sf"><b>sigma_sf (double precision)</b></a>
<ul>
<li> σ parameter for the interaction between this atom and the wall atoms. Units are Angstroms.</li>
</ul>
</dt>
<dt><a name="epsilon_sf"><b>epsilon_sf (double precision)</b></a>
<ul>
<li> ε parameter for the interaction between this atom and the wall atoms. Units are K/k<sub>B</sub>.</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</dt>
</ul>
</li>
<li>'external': calls an external code (compiled as a library) that computes the total energy of the system.
When using this option you need to include the following variable.
<ul>
<dt><a name="external_code"><b>external_code (character*20)</b></a>
<ul>
<li>'lcao': uses the lcao code of Peter Schultz, also known as <a href="http://dft.sandia.gov/Quest/">Quest</a> or SeqQuest, to compute the
quantum mechanical energy. Use of this option requires the placement of several libraries into the /towheebase/lib directory (use of symbolic
links is also acceptable in that directory). The code must be compiled with the '--enable-lcao' option in order to link in these libraries.
When using this option you must also include the following variables.
<ul>
<dt><a name="lcao_functional"><b>lcao_functional</b> (character*20)</b></a>
<ul>
<li>'LDA': uses the local density approximation to compute the energy.</li>
</ul>
</dt>
<dt><a name="lcao_atomtypes"><b>lcao_atomtypes (integer)</b></a>
<ul>
The number of different elements used in the quantum code.
</ul>
</dt>
<dt><a name="lcao_filename"><b>lcao_filename (character*50 array)</b></a>
<ul>
A list of the atom filenames used in Quest. Listed one on a line for each atom type.
</ul>
</dt>
<dt><a name="lcao_gridmultiplier"><b>lcao_gridmultiplier (double precision)</b></a>
<ul>
Value that is multiplied by the box dimensions in order to compute the lcao grid dimensions. Suggested value is 4.0.
</ul>
</dt>
<dt><a name="lcao_kgridproduct"><b>lcao_kgridproduct (double precision)</b></a>
<ul>
This value is divided by the box dimensions in order to compute the lcao kgrid. Suggested value is 40.0.
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="solvation_style"><b>solvation_style (character*20)</b> <em>optional parameter</em></a>
<ul>
<li>'none' : no additional solvation potential for this system (default value).</li>
<li>'internal' : use one of the solvation potentials internal to Towhee. This option requires the following variable.
<ul>
<dt><a name="solvation_type"><b>solvation_type (character*20)</b></a>
<ul>
<li>'EEF1' : solvation using the Charmm19-EEF1 potential.</li>
</ul>
</dt>
</ul>
</li>
<li>'external' : use a solvation potential via an external program that has been compiled as a library and linked into Towhee.
<ul>
<dt><a name="solvation_type"><b>solvation_type (character*20)</b></a>
<ul>
<li>'tramonto' : solvation using the classical density functional theory code Tramonto to compute a solvation free energy.</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="linit"><b>linit (logical)</b></a>
<ul>
<li> .TRUE. if you are starting the simulation and wish to generate the positions of all of the atoms, assign initial box lengths and
maximum displacements.
</li>
<li> .FALSE. if you want to continue the simulation by reading in box lengths, maximum displacements, and coordinates from towhee_initial.</li>
</ul>
</dt>
<dt><a name="initboxtype"><b>initboxtype (character*20)</b></a>
<ul>
<li>'unit cell': generates an initial structure by duplicating a unit cell. Reads information from the towhee_cell file and uses that to create
an initial structure.
</li>
<li>'dimensions': the dimensions of the initial boxes are entered in order to construct the initial boxes.</li>
<li>'number density': the total number density of molecules in the initial boxes are entered in order to compute the initial sizes of the boxes.
This option generates cubic boxes.
</li>
</ul>
</dt>
<dt><a name="initstyle"><b>initstyle (character*20)</b></a>
<dt>This variable is only required for <b>initboxtype</b> settings of 'dimensions' or 'number density'</dt>
<ul>
One line for each simulation box in the system. Each line contains a value for each molecule type.
<li>'full cbmc': A template for this molecule type is created using configurational-bias. This template is then replicated throughout the simulation
box to generate an initial configuration.
</li>
<li>'template': A template for this molecule type is read from <a href="../usersmanual.html#towhee_template">towhee_template</a>.
This template is then replicated throughout the simulation box to generate an initial configuration.
</li>
<li>'coords': The coordinates for each atom are read from <a href="../usersmanual.html#towhee_coords">towhee_coords</a>.
This is useful if you are starting from a different file format (such as pdb), or have another code for building an initial configuration.
</li>
<li>'nanotube': The coordinates for each atom are read from towhee_nanotube. This file is generated by the Towhee code if you use the inpstyle for
carbon nanotubes. This template is then replicated throughout the simulation box to generate an initial conformation.
</li>
<li>'helix cbmc': The molecule is generated by placing some of the backbone atoms onto a helix and then growing the rest of the atoms using CBMC.
Any molecule initialized using this style must have the following information listed subsequent to the <b>initstyle</b> variables.
<ul>
<dt><a name="helix_moltyp"><b>helix_moltyp (integer)</b></a>
<ul>
An integer corresponding to the molecule type that had an <b>initstyle</b> variable set to 4 in one of the simulation boxes. These must be
listed in consecutive order.
</ul>
</dt>
<dt><a name="helix_radius"><b>helix_radius (double precision)</b></a>
<ul>
The radius of the helix (units of Angstroms).
</ul>
</dt>
<dt><a name="helix_angle"><b>helix_angle (double precision)</b></a>
<ul>
The pitch angle the helix makes with respect to the z-axis (units of degrees).
</ul>
</dt>
<dt><a name="helix_keytype"><b>helix_keytype (character*10)</b></a>
<ul>
<li>'element' compares the <b>helix_keyname</b> with the character*2 variable element that contains the 2 letter elemental code for each atom.</li>
<li>'nbname' compares the <b>helix_keyname</b> with the character*10 variable nbname that contains the 10 character code for each atom type.
This is the same variable that is used when inputting the atom names with the Atom-based connectivity map (<b>inpstyle</b>=2).
</li>
<li>'pdbname' compares the <b>helix_keyname</b> with the character*4 variable pdbname that contains the 4 character code used in the pdb format
output. This is most suitable for use with the Polypeptide builder (<b>inpstyle</b>=1) or the Nucleic acid builder (<b>inpstyle</b>=4).
</li>
</ul>
</dt>
<dt><a name="helix_keyname"><b>helix_keyname (character*10)</b></a>
<ul>
The key for finding matches of the atom with the data structures for the molecule that is being grown as a helix. You need to choose an atom name
that only appears in the backbone (e.g. 'P' for Charmm27 nucleic acids when using the element keytype, or ' CA ' for the C alpha backbone carbon
of a polypeptide when using the pdbname keytype).
</ul>
</dt>
<dt><a name="helix_conlen"><b>helix_conlen (double precision)</b></a>
<ul>
The distance between consecutive <b>helix_element</b> atoms (units of Angstroms).
</ul>
</dt>
<dt><a name="helix_phase"><b>helix_phase (double precision)</b></a>
<ul>
The initial angle of the helical chain (units of degrees). Normally, this has little effect as it is just a rotation about the z-axis, but
if you are trying to set up two complementary nucleic acid chains to form a double helix then you would want their phase angles to differ
by 180 degrees.
</ul>
</dt>
</ul>
</li>
<li>'partial cbmc': The molecule is constructed in two steps. First, a partial list of atom positions, amino acid 3-letter codes, and 4-letter atom
identifiers (following the pdb standard) is read from towhee_partial and matched up against the expected amino acid and atom codes from the
molecule template listed in towhee_input. Then configurational-bias is used to grow all of the missing atoms to create the initial structure.
</li>
</ul>
</dt>
<dt><a name="initlattice"><b>initlattice (character*20)</b></a>
<dt>This variable is only required for <b>initboxtype</b> settings of 'dimensions' or 'number density'.</dt>
<ul>
One line for each simulation box in the system. Each line contains a value for each molecule type.
<li>'center': puts the center of mass of the molecule in the very center of the box. This is a very poor idea if you have multiples of the same
molecule type in a box as they will all be right on top of each other. However, it is useful if you are trying to get multiple different molecule
types in an initial configuration where one molecule is inside of another (multi-walled nanotubes is a good example).
</li>
<li>'none': place the molecules exactly where their template indicates. This option makes the most sense for <b>initstyle</b> options like 'coords'
where you want to just read positions from a file.
</li>
<li>'simple cubic': places the first atom of the molecule onto a simple cubic lattice and the rest of the atoms in the molecule are placed relative to
that atom. If you are not using an <b>initstyle</b> of 'coords' then this is probably the option you want to use to generate an initial structure.
</li>
</ul>
</dt>
<dt><a name="initmol"><b>initmol (integer)</b></a>
<dt>This variable is only required for <b>initboxtype</b> settings of 'dimensions' or 'number density'</dt>
<ul>
<li> The initial number of each type of molecule in each box (one line per box).</li>
</ul>
</dt>
<dt><a name="inix"><b>inix, iniy, iniz (integer)</b></a>
<ul>
<li> The initial number of molecules (for <b>initboxtype</b> settings of 'dimensions' or 'number density') or of duplicated unit cells
(for <b>initboxtype</b> setting of 'unit cell') in each direction in each box. The product of inix*iniy*iniz must be greater than or equal to the
initial number of molecules in that box (for <b>initboxtype</b> settings of 'dimensions' or 'number density'). While these are labeled x, y, and z
they actually correspond to the three coordinate vectors (truly x, y, and z for a rectangular box).
</li>
</ul>
</dt>
<dt><a name="hmatrix"><b>hmatrix (double precision)</b></a>
<dt>This variable is only required for <b>initboxtype</b> settings of 'dimensions'</dt>
<ul>
<li> The initial box dimensions (Angstroms) for the three vectors that describe the simulation box. There are nine entries (3 for each of the
3 vectors) in total for each simulation box. These are listed one vector at a time, with the three numbers which make up each vector listed on the
same line. Note that the coordinate system you choose does not have to be orthogonal, but it must follow the right hand rule. The three vectors
must also all be at least 45 degrees apart. Note that if you wish to use a rectangular box then only the diagonal elements of hmatrix will be
non-zero, and these will be equal to the box lengths in the x, y, and z dimensions.
</li>
</ul>
</dt>
<dt><a name="box_number_density"><b>box_number_density (double precision)</b></a>
<dt>This variable is only required for <b>initboxtype</b> settings of 'number density'</dt>
<ul>
<li>The initial total number density of molecules in each simulation box. Listed as a single value per line with one line for each box as specified
by <b>numboxes</b>. Units are molecules per nm<sup>3</sup>.
</li>
</ul>
</dt>
<hr></hr>
<a name="pm_header">
<li>Note: the pm* variables are used to determine which move type to perform every time we want to do a Monte Carlo move. A move is selected
by choosing a random number between 0.0 and 1.0 and then going down the list of pm* until you find one which has a value higher than the random number.
At least one of the variables must be set to 1.0. A similar procedure is performed when we want to determine which boxes or molecule types
to perform the selected move upon. These are done using the pm**pr and pm**mt arrays.
<p></p>
Starting with Towhee release 4.15.2, all leading pm* probabilities are optional; if such a probability is not specified, then the rest of the variables
in that section must likewise be left out, and the probability of that move is zero. As an example, if the variable <b>pmback</b> is not given, then
<b>pmbkmt</b> must not be specified, and the <em>Configurational-Bias Protein Backbone Regrowth</em> move will never be performed.
</li>
<hr></hr>
<dt>Isotropic Volume Move: These variables are only included for the following cases
<ul>
<li><b>ensemble</b> is 'npt'</li>
<li><b>ensemble</b> is 'nvt' and <b>numboxes</b> is 2 or more.</li>
</ul>
<dt><a name="pmvol"><b>pmvol (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a volume move. If (<b>ensemble</b> is 'npt') then a single box is selected and it exchanges volume with an external
pressure bath (see pressure). If (<b>ensemble</b> = 'nvt' and numboxes > 1) a pair of boxes are selected and volume is exchanged between them.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmvlpr"><b>pmvlpr (double precision)</b></a>
<ul>
<li> Probability of performing a volume move on a particular box, or box pair. All of these variables are listed on a single line.
If (<b>ensemble</b> = 'npt') then a value of pmvlpr is listed for each box.
If (<b>ensemble</b> = 'nvt') then a value is listed for each pair of simulation boxes where the pairs are ordered (1,2), (1,3), ... (1,numboxes),
(2,3), ... (numboxes-1,numboxes).
</li>
</ul>
</dt>
<dt><a name="rmvol"><b>rmvol (double precision) [a single value regardless of the actual number of box pairs]</b></a>
<ul>
<li> The initial volume maximum displacement. If this is an isobaric-isothermal ensemble (<b>ensemble</b> = 'npt') then this is the initial maximum
volume displacement (cubic Angstroms) in each box. If this is the canonical Gibbs ensemble (<b>ensemble</b> = 'nvt' and numboxes > 1 )
then this is the maximum displacement (logarithmic space) for each pair of boxes. As the simulation progresses, these values will be updated for
each box, or each pair of boxes (see iratv).
</li>
</ul>
</dt>
<dt><a name="tavol"><b>tavol (double precision)</b></a>
<ul>
<li> The target acceptance rate for the volume move. Must be a value between 0.0 and 1.0. The volume displacement (rmvol) is periodically
adjusted (see iratv) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Anisotropic Volume Move: These variables are only included for the following cases
<ul>
<li><b>ensemble</b> is 'npt'</li>
<li><b>ensemble</b> is 'nvt' and <b>numboxes</b> is 2 or more.</li>
</ul>
<dt><a name="pmcell"><b>pmcell (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a unit cell adjustment move. If (<b>ensemble</b> = 'npt' ) then a single box is selected and a single hmatrix element
is changed. This results in a volume exchange with a fictional external pressure bath (see pressure).
If (<b>ensemble</b> = 'nvt' and numboxes > 1) a pair of boxes are selected. One of the boxes is then selected according to the pmcellpt
variable and a single hmatrix element is changed in that box. This results in a change of volume for the first box which is countered by
isotropically changing the volume in the second box.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmcellpr"><b>pmcellpr (double precision)</b></a>
<ul>
<li> Probability of performing a unit cell adjustment move on a particular box, or box pair. All of these variables are listed on a single line
If (<b>ensemble</b> = 'npt') then a value of pmvlpr is listed for each box. If (<b>ensemble</b> = 'nvt') then a value is listed for each pair of
simulation boxes where the pairs are ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
</li>
</ul>
</dt>
<dt><a name="pmcellpt"><b>pmcellpt (double precision)</b></a>
<ul>
<li> Probability of selecting the first box of the pair as the box to perform the non-isotropic volume move upon, while its partner undergoes an
isotropic volume move. This variable is only meaningful if (<b>ensemble</b> = 'nvt'). Note that you can choose to perform the non-isotropic
volume move always on the same box and this might be useful if you are doing a solid-vapor equilibria calculation.
</li>
</ul>
</dt>
<dt><a name="rmcell"><b>rmcell (double precision)</b></a>
<ul>
<li> The initial unit cell adjustment maximum displacement. In all cases, this is the maximum amount (in Angstroms) that a single element of the
hmatrix can change in a single unit cell move. Note, the in the canonical Gibbs ensemble case it is possible for the isotropic box to undergo an
hmatrix change that is larger than this value as that box simply makes up for the volume change caused by the non-isotropic adjustment in the
first box. As the simulation progresses, these values are updated for each box with a frequency controlled by <b>iratv</b>.
</li>
</ul>
</dt>
<dt><a name="tacell"><b>tacell (double precision)</b></a>
<ul>
<li> The target acceptance rate for the unit cell adjustment move. Must be a value between 0.0 and 1.0. The unit cell displacement (rmcell) is
periodically adjusted (see iratv) to yield this acceptance rate. I typically use a value of 0.5.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Rotational-bias 2 box molecule Transfer Move: These variables are only included if <b>numboxes</b> is greater than or equal to 2
<dt><a name="pm2boxrbswap"><b>pm2boxrbswap (double precision)</b> <em>optional parameter</em></a>
<ul>
<li>Probability of performing a rotational-bias interbox molecule transfer move. This move takes a molecule out of one box and tries to place it
in another box. The molecule is grown using <b>nch_nb_one</b> attempted different orientations and position (of the center-of-mass) for the new
molecule.
</li>
</ul>
</dt>
<ul>
<dt><a name="pm2rbswmt"><b>pm2rbswmt (double precision)</b></a>
<ul>
<li>Probability of performing a rotational-bias interbox molecule transfer move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="pm2rbswpr"><b>pm2rbswpr (double precision)</b></a>
<ul>
<li> Probability of performing a rotational-bias interbox molecule transfer move between each pair of boxes in the system. The box pairs are
ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-bias 2 box molecule Transfer Move: These variables are only included if <b>numboxes</b> is greater than or equal to 2
<dt><a name="pm2boxcbswap"><b>pm2boxcbswap (double precision)</b> <em>optional parameter</em></a>
<ul>
<li>Probability of performing a configurational-bias interbox molecule transfer move. This move takes a molecule out of one box and tries
to place it in another box. The molecule is grown using <a href="../algorithm/cbmc.html">coupled-decoupled configurational-bias Monte Carlo</a>.
</li>
</ul>
</dt>
<ul>
<dt><a name="pm2cbswmt"><b>pm2cbswmt (double precision)</b></a>
<ul>
<li>Probability of performing a configurational-bias interbox molecule transfer move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="pm2cbswpr"><b>pm2cbswpr (double precision)</b></a>
<ul>
<li> Probability of performing a configurational-bias interbox molecule transfer move between each pair of boxes in the system. The box pairs are
ordered (1,2), (1,3), ... (1,numboxes), (2,3), ... (numboxes-1,numboxes).
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-bias grand-canonical insertion/deletion Move: These variables are only included if <b>ensemble</b> is 'uvt'
<dt><a name="pmuvtcbswap"><b>pmuvtcbswap (double precision)</b> <em>optional parameter</em></a>
<ul>
<li>Probability of performing a grand-canonical configurational-bias insertion or deletion move.</li>
</ul>
</dt>
<ul>
<dt><a name="pm2cbswpr"><b>pmuvtcbmt (double precision)</b></a>
<ul>
<li>Probability of performing a grand-canonical configurational-bias insertion or deletion move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-bias single box molecule Reinsertion Move
<dt><a name="pm1boxcbswap"><b>pm1boxcbswap (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing an intrabox configurational-bias molecule transfer move. This move takes a molecule out of one box and tries to place
it back into the same box. The molecule is grown using <a href="../algorithm/cbmc.html">coupled-decoupled configurational-bias Monte Carlo</a>.
</li>
</ul>
</dt>
<ul>
<dt><a name="pm1cbswmt"><b>pm1cbswmt (double precision)</b></a>
<ul>
<li> Probability of performing an intrabox configurational-bias molecule transfer move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Intrabox two molecule switch based upon the center of mass positions
<dt><a name="pm1boxcomswitch"><b>pm1boxcomswitch (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing an intrabox exchange of the center of mass of two molecules of different types.
</li>
</ul>
</dt>
<ul>
<dt><a name="pm1comswbox"><b>pm1comswbox (double precision)</b></a>
<ul>
<li> Probability of performing a center of mass switch move in each simulation box. List one value for each simulation box. At least one of the
boxes must have a value of 1.0d0.
</ul>
</dt>
<dt><a name="pm1comswpair"><b>pm1comswpair (double precision)</b></a>
<ul>
<li> Probability of performing a center of mass switch move on each pair of molecule types in the simulation.
List one value for each pair of molecule types in the simulation (<b>nmolty</b>*(<b>nmolty</b>-1)/2).
At least one of the pairs must have a value of 1.0d0.
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Aggregation Volume Bias Move Type 1
<dt><a name="pmavb1"><b>pmavb1 (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 1, as described in
<a href="../references.html#chen_siepmann_2000">Chen and Siepmann 2000</a>. This is useful for forming and destroying clusters in simulations with
molecules that tend to aggregate together.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmavb1in"><b>pmavb1in (double precision)</b></a>
<ul>
<li> Probability of trying to move a molecule into an inner region for aggregation volume bias move of type 1.</li>
</ul>
</dt>
<dt><a name="pmavb1mt"><b>pmavb1mt (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 1 where a molecule of a certain type is moved.
This is an array with one element for each molecule type.
</li>
</ul>
</dt>
<dt><a name="pmavb1ct"><b>pmavb1ct (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 1 where the molecule target is of a certain type. The molecule that is
moved is chosen according to <b>pmavb1mt</b> and then the type of molecule that is used as a reference for determining the inner and outer regions
is found using this variable. This is a two dimensional array and uses one line of text for each type of molecule in the system.
</li>
</ul>
</dt>
<dt><a name="avb1rad"><b>avb1rad (double precision)</b></a>
<ul>
<li> The radius used to define the inner and outer volumes in the aggregation volume bias move of type 1. The distance is specified in Angstroms
and must be greater than zero, but less than or equal to <b>rcut</b>.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Aggregation Volume Bias Move Type 2
<dt><a name="pmavb2"><b>pmavb2 (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 2, as described in
<a href="../references.html#chen_siepmann_2001">Chen and Siepmann 2001</a>.
This is useful for forming and destroying clusters in simulations with molecules that tend to aggregate together.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmavb2in"><b>pmavb2in (double precision)</b></a>
<ul>
<li> Probability of trying to move a molecule into an inner region for aggregation volume bias move of type 2.</li>
</ul>
</dt>
<dt><a name="pmavb2mt"><b>pmavb2mt (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 2 where a molecule of a certain type is moved. This is an array with one
element for each molecule type.
</li>
</ul>
</dt>
<dt><a name="pmavb2ct"><b>pmavb2ct (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 2 where the molecule target is of a certain type. The molecule that is moved
is chosen according to <b>pmavb2mt</b> and then the type of molecule that is used as a reference for determining the inner and outer regions is
found using this variable. This is a two dimensional array and uses one line of text for each type of molecule in the system.
</li>
</ul>
</dt>
<dt><a name="avb2rad"><b>avb2rad (double precision)</b></a>
<ul>
<li> The radius used to define the inner and outer volumes in the aggregation volume bias move of type 2. The distance is specified in Angstroms
and must be greater than zero, but less than or equal to <b>rcut</b>.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Aggregation Volume Bias Move Type 3
<dt><a name="pmavb3"><b>pmavb3 (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 3, as described in
<a href="../references.html#chen_siepmann_2001">Chen and Siepmann 2001</a>. This is useful for transferring molecules between clusters.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmavb3mt"><b>pmavb3mt (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 3 where a molecule of a certain type is moved.
This is an array with one element for each molecule type.
</li>
</ul>
</dt>
<dt><a name="pmavb3ct"><b>pmavb3ct (double precision)</b></a>
<ul>
<li> Probability of performing an aggregation volume bias move of type 3 where the molecule target is of a certain type. The molecule that is moved
is chosen according to <b>pmavb1mt</b> and then the type of molecule that is used as a reference for determining the inner and outer regions is
found using this variable. This is a two dimensional array and uses one line of text for each type of molecule in the system.
</li>
</ul>
</dt>
<dt><a name="avb3rad"><b>avb3rad (double precision)</b></a>
<ul>
<li> The radius used to define the inner and outer volumes in the aggregation volume bias move of type 3. The distance is specified in Angstroms
and must be greater than zero, but less than or equal to <b>rcut</b>.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-Bias Partial Molecule Regrowth
<dt><a name="pmcb"><b>pmcb (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a molecule regrowth move on a molecule without regard to which box the molecule is currently located in. This move
chooses a molecule of the appropriate type at random, selects an atom of the molecule at random, and then regrows the molecule either entirely
(if a random number < pmall) or in all directions except for one.
The molecule is regrown using <a href="../algorithm/cbmc.html">configurational-bias</a>.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmcbmt"><b>pmcbmt (double precision)</b></a>
<ul>
<li> Probability of performing a molecule regrowth on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="pmall"><b>pmall (double precision)</b></a>
<ul>
<li> pmall is the probability that a molecule regrowth move will regrow the entire molecule. This is listed for each molecule type in the
simulation.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-Bias Protein Backbone Regrowth
<dt><a name="pmback"><b>pmback (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing configurational-bias fixed-endpoint regrowth of a portion of the protein backbone. This selects an atom along the
peptide backbone, chooses another backbone atom that is connected by three bonds to the first atom, and then regrows all of the atoms in between
these two atoms.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmbkmt"><b>pmbkmt (double precision)</b></a>
<ul>
<li> Probability of performing a backbone regrowth move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Configurational-Bias Peptide side-chain Regrowth
<dt><a name="pmcbside"><b>pmcbside (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a configurational-bias regrowth move on a single side-chain of peptide. This works by compiling a list of
atoms that have a pdbname of ' CA ' and selecting one of those at the origin of a side-chain regrowth. This is functional for the normal amino
acids, plus proline and disulfide bonded cysteines.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmcbsidemt"><b>pmcbsidemt (double precision)</b></a>
<ul>
<li> Probability of performing a configurational-bias side-chain regrowth on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Torsional Pivot Move
<dt><a name="pmpivot"><b>pmpivot (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a pivot move about a random bond in the molecule. This move chooses a bond that is not entirely contained in a
single ring structure, and has at least one bond emanating from each end, and then rotates one side of the molecule about that bond.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmpivmt"><b>pmpivmt (double precision)</b></a>
<ul>
<li> Probability of performing a pivot move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Concerted Rotation Move on a non-peptide backbone
<dt><a name="pmconrot"><b>pmconrot (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a concerted rotation move for a sequence of 9 atoms in a molecule.</li>
</ul>
</dt>
<ul>
<dt><a name="pmcrmt"><b>pmcrmt (double precision)</b></a>
<ul>
<li> Probability of performing a concerted rotation move move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Concerted Rotation Move over a 3 peptides backbone sequence
<dt><a name="pmcrback"><b>pmcrback (double precision)</b> <em>optional parameter</em></a>
<ul>
<li>Probability of performing a concerted rotation move on a sequence of three peptides in a polypeptide.
This move only works for polypeptides.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmcrbmt"><b>pmcrbmt (double precision)</b></a>
<ul>
<li> Probability of performing a protein backbone concerted rotation move on each type of molecule in the system.</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Plane Shift Move
<dt><a name="pmplane"><b>pmplane (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a plane shift move. This move displaces all of the molecules whose center of mass lies in a plane of width
<b>planewidth</b>. A new trial position for the center of the plane of atoms is generated uniformly across the available plane.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmplanebox"><b>pmplanebox (double precision)</b></a>
<ul>
<li> Probability of performing a plane shift in each of the simulation boxes. List one value for each simulation box. At least one of the
boxes must have a value of 1.0d0.
</li>
</ul>
</dt>
<dt><a name="planewidth"><b>planewidth (double precision)</b></a>
<ul>
<li> The width of the plane for the plane shift move. Any molecule whose center of mass is within a plane of this thickness (whose position is
chosen uniformly along one axis) will move during the plane shift move. The value of planewidth must be greater than 0.0d0 and less than the
shortest box length.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Row Shift Move
<dt><a name="pmrow"><b>pmrow (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a row shift move. This move displaces all of the molecules whose center of mass lies in a row of diameter
<b>rowwidth</b>. A new trial position for the center of the row of atoms is generated uniformly across the available row.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmrowbox"><b>pmrowbox (double precision)</b></a>
<ul>
<li> Probability of performing a row shift in each of the simulation boxes. List one value for each simulation box. At least one of the boxes
must have a value of 1.0d0.
</li>
</ul>
</dt>
<dt><a name="rowwidth"><b>rowwidth (double precision)</b></a>
<ul>
<li> The width of the plan for the row shift move. Any molecule whose center of mass is within a row of this thickness (whose position is chosen
uniformly along one axis) will move during the row shift move. The value of rowwidth must be greater than 0.0d0 and less than the shortest
box length.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Intramolecular Single Atom Translation Move
<dt><a name="pmtraat"><b>pmtraat (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a single-atom translation move on a molecule without regard to which box the molecule is currently located in. This
move chooses a molecule of the appropriate type at random, selects an atom of the molecule at random, selects a vector on a unit sphere at random,
and then attempts to displace the atom a random distance between -rmtraa and +rmtraa in that direction.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmtamt"><b>pmtamt (double precision)</b></a>
<ul>
<li> Probability of performing a single-atom translation move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="rmtraa"><b>rmtraa (double precision)</b></a>
<ul>
<li> The initial Atom-translation maximum displacement (Angstroms) for all molecules types in all boxes. As the simulation progresses, these values
are updated to yield the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
</li>
</ul>
</dt>
<dt><a name="tatraa"><b>tatraa (double precision)</b></a>
<ul>
<li> The target acceptance rate for the atom translation move. Must be a value between 0.0 and 1.0. The maximum atom translational displacement
(rmtraa) is periodically adjusted (see trmaxdispfreq) to yield this acceptance rate. I typically use a value of 0.5, though some researchers
prefer smaller values.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Composite Move
<dt><a name="pmcomposite"><b>pmcomposite (double precision)</b></a> <em>optional parameter</em>
<ul>
<li> Probability of performing a composite move that consists of a random center-of-mass translation and random rotation. This move is essentially
a concatenation of the Center-of-Mass Molecule Translation Move and the Rotation about the Center-of-Mass Move.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmcomt"><b>pmcomt (double precision)</b></a>
<ul>
<li> Probability of performing a composite move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="rmcomtra"><b>rmcomtra (double precision)</b></a>
<ul>
<li> The molecular translation displacement (angstroms) for all molecule types in all boxes. This parameter is essentially identical
to the <b><a href="#rmtrac">rmtrac</a></b> parameter for translations of molecular COM.
</li>
</ul>
</dt>
<dt><a name="rmcomrot"><b>rmcomrot (double precision)</b></a>
<ul>
<li> The molecular rotation maximum displacement (radians) for all molecule types in all boxes. This parameter is essentially identical to the
<b><a href="#rmrot">rmrot</a></b> parameter for rotations about COM.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Center-of-Mass Molecule Translation Move
<dt><a name="pmtracm"><b>pmtracm (double precision)</b> <em>optional parameter</em></a>
<ul>
<li> Probability of performing a center-of-mass translation move on a molecule without regard to which box the molecule is currently located in.
This move chooses a molecule of the appropriate type at random, chooses a vector on a unit sphere at random, and then attempts to displace the
entire molecule a random distance between -rmtrac and +rmtrac in that direction.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmtcmt"><b>pmtcmt (double precision)</b></a>
<ul>
<li> Probability of performing a center-of-mass translation move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="rmtrac"><b>rmtrac (double precision)</b></a>
<ul>
<li> The initial Center-of-mass translation maximum displacement (Angstroms) for all molecule types in all boxes. As the simulation progresses,
these values are updated to yield the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
</li>
</ul>
</dt>
<dt><a name="tatrac"><b>tatrac (double precision)</b></a>
<ul>
<li> The target acceptance rate for the center-of-mass translation move. Must be a value between 0.0 and 1.0. The maximum center-of-mass
translational displacement (rmtrac) is periodically adjusted (see trmaxdispfreq) to yield this acceptance rate. I typically use a value of
0.5, though some researchers prefer smaller values.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt>Rotation about the Center-of-Mass Move
<dt><a name="pmrotate"><b>pmrotate (double precision)</b></a> <em>optional parameter</em>
<ul>
<li> Probability of performing a rotation about the center-of-mass move for a molecule without regard to the box the molecule is currently
located in. This move chooses a molecule of the appropriate type at random and then attempts to rotate the entire molecule about the x, y, and z
axes that run through the center-of-mass a random number of radians between -<b>rmrot</b> and +<b>rmrot</b> around each of the three axes.
</li>
</ul>
</dt>
<ul>
<dt><a name="pmromt"><b>pmromt (double precision)</b></a>
<ul>
<li> Probability of performing a rotation move on each type of molecule in the system.</li>
</ul>
</dt>
<dt><a name="rmrot"><b>rmrot (double precision)</b></a>
<ul>
<li> The initial molecular rotation maximum displacement (radians) for all molecule types in all boxes. As the simulation progresses, these values
are updated to yield the desired acceptance rate for each molecule type in each box (see trmaxdispfreq).
</li>
</ul>
</dt>
<dt><a name="tarot"><b>tarot (double precision)</b></a>
<ul>
<li> The target acceptance rate for the rotation move. Must be a value between 0.0 and 1.0. The rotation displacement (rmrot) is periodically
adjusted (see trmaxdispfreq) to yield this acceptance rate. I typically use a value of 0.5, though some researchers prefer smaller values.
</li>
</ul>
</dt>
</ul>
</dt>
<hr></hr>
<dt><a name="cbmc_formulation"><b>cbmc_formulation (character*60)</b></a> <em>optional parameter</em>
<ul>
<li>'Martin and Frischknecht 2006': (<font color="red">Current default setting</font>) Monte Carlo moves that involve the
<a href="../algorithm/cbmc.html">configurational-bias</a>
algorithm use the Coupled to pre-nonbond formulation of the coupled-decoupled algorithm that is described in
<a href="../references.html#martin_frischknecht_2006">Martin and Frischknecht 2006</a>.
This algorithm has a bond length selection, two bending angle selections, and a dihedral selection that are all decoupled from each other; while in
turn being coupled to a pre-nonbond loop that is coupled to the nonbonded selection.
</li>
<li>'Martin and Siepmann 1999 + Martin and Thompson 2004': Monte Carlo moves that involve the <a href="../algorithm/cbmc.html">configurational-bias</a>
algorithm use the coupled-decoupled formulation presented in the appendix of
<a href="../references.html#martin_siepmann_1999">Martin and Siepmann 1999</a> with the
addition of a decoupled bond selection first described in <a href="../references.html#martin_thompson_2004">Martin and Thompson 2004</a>.
This algorithm has decoupled bond length selection, two decoupled angle selections, and a dihedral selection that is coupled to the nonbonded
selection.
</li>
</ul>
</dt>
<dt><a name="cbmc_setting_style"><b>cbmc_setting_style (character*30)</b></a> <em>optional parameter</em>
<ul>
<li>'Martin and Frischknecht': (<font color="red">Current default setting</font>) sets up the configurational-bias values according to the strategies
described in
<a href="../references.html#martin_frischknecht_2006">Martin and Frischknecht 2006</a>. This option sets the following variables for all molecule
types in the system. For more information about these variables see the explicit setting for this variable.
<ul>
<dt><b>cbmc_bond_generation</b> = 'autofit gaussian'</dt>
<dt><b>bond_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>cbmc_bend_generation</b> = 'ideal + autofit gaussian'</dt>
<dt><b>bend_a_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>bend_b_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>bend_a_ideal_fraction</b> = 0.01d0</dt>
<dt><b>bend_b_ideal_fraction</b> = 0.01d0</dt>
<dt><b>cbmc_dihedral_generation</b> = 'ideal + autofit gaussian'</dt>
<dt><b>dihedral_peak_weight_style</b> = 'uniform'</dt>
<dt><b>dihedral_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>dihedral_ideal_fraction</b> = 0.01d0</dt>
<dt><b>cbmc_nb_one_generation</b> = 'uniform'</dt>
<dt><b>two_bond_fixed_endpoint_bias_style</b> = 'analytic Boltzmann using angles'</dt>
<dt><b>three_bond_fixed_endpoint_bias_style</b> = 'analytic using max and min 2-4 distance'</dt>
<dt><b>nch_nb_one</b> = 10</dt>
<dt><b>nch_nb</b> = 10</dt>
<dt>if <b>cbmc_formulation</b> = 'Martin and Siepmann 1999 + Martin and Thompson 2004' then
<ul>
<dt><b>nch_pre_nb</b> = 1</dt>
<dt><b>nch_tor</b> = 100</dt>
<dt><b>nch_tor_connect</b> = 100</dt>
<dt><b>nch_bend_b</b> = 100</dt>
</ul>
</dt>
<dt>else if <b>cbmc_formulation</b> = 'Martin and Frischknecht 2006' then
<ul>
<dt><b>nch_pre_nb</b> = 100</dt>
<dt><b>nch_tor</b> = 1</dt>
<dt><b>nch_tor_connect</b> = 1</dt>
<dt><b>nch_bend_b</b> = 1</dt>
</ul>
</dt>
<dt><b>nch_bend_a</b> = 1</dt>
<dt><b>nch_vib</b> = 1</dt>
</ul>
</li>
<li>'default ideal': sets up all of the configurational-bias variables according to a general set of default values using the 'ideal' generation
styles. This option sets the following variables for all molecule types in the system. For more information about these variables see the explicit
setting for this variable).
<ul>
<dt><b>cbmc_bond_generation</b> = 'r^2 with bounds'</dt>
<dt><b>cbmc_bend_generation</b> = 'ideal'</dt>
<dt><b>cbmc_dihedral_generation</b> = 'ideal'</dt>
<dt><b>cbmc_nb_one_generation</b> = 'uniform'</dt>
<dt><b>two_bond_fixed_endpoint_bias_style</b> = 'analytic Boltzmann using angles and dihedrals'</dt>
<dt><b>three_bond_fixed_endpoint_bias_style</b> = 'analytic using max and min 2-4 distance'</dt>
<dt><b>nch_nb_one</b> = 10</dt>
<dt><b>nch_nb</b> = 10</dt>
<dt><b>nch_pre_nb</b> = 1</dt>
<dt><b>nch_tor</b> = 360</dt>
<dt><b>nch_tor_connect</b> = 360</dt>
<dt><b>nch_bend_a</b> = 1000</dt>
<dt><b>nch_bend_b</b> = 1000</dt>
<dt><b>nch_vib</b> = 1000</dt>
<dt><b>vibrang</b> = 0.85 1.15</dt>
</ul>
</li>
<li>'widom ideal': sets up all of the configurational-bias variables according to a general set of default values using the 'ideal' generation styles
in such a manner that the chemical potential is computed correctly using the normal widom insertion. This option sets the following variables for
all molecule types in the system. For more information about these variables see the explicit setting for this variable).
<ul>
<dt><b>cbmc_bond_generation</b> = 'r^2 with bounds'</dt>
<dt><b>cbmc_bend_generation</b> = 'ideal'</dt>
<dt><b>cbmc_dihedral_generation</b> = 'ideal'</dt>
<dt><b>cbmc_nb_one_generation</b> = 'uniform'</dt>
<dt><b>two_bond_fixed_endpoint_bias_style</b> = 'none'</dt>
<dt><b>three_bond_fixed_endpoint_bias_style</b> = 'none'</dt>
<dt><b>nch_nb_one</b> = 1</dt>
<dt><b>nch_nb</b> = 1</dt>
<dt><b>nch_pre_nb</b> = 1</dt>
<dt><b>nch_tor</b> = 360</dt>
<dt><b>nch_tor_connect</b> = 360</dt>
<dt><b>nch_bend_a</b> = 1000</dt>
<dt><b>nch_bend_b</b> = 1000</dt>
<dt><b>nch_vib</b> = 1000</dt>
<dt><b>vibrang</b> = 0.85 1.15</dt>
</ul>
</li>
<li>'Martin and Thompson FPE 2004': sets up all of the configurational-bias variables to the values used in
<a href="../references.html#martin_thompson_2004">Martin and Thompson 2004</a>. This option sets the following variables for all molecule types
in the system. For more information about these variables see the explicit setting for this variable).
<ul>
<dt><b>cbmc_bond_generation</b> = 'r^2 with bounds'</dt>
<dt><b>cbmc_bend_generation</b> = 'ideal'</dt>
<dt><b>cbmc_dihedral_generation</b> = 'ideal'</dt>
<dt><b>cbmc_nb_one_generation</b> = 'uniform'</dt>
<dt><b>two_bond_fixed_endpoint_bias_style</b> = 'analytic Boltzmann using angles and dihedrals'</dt>
<dt><b>three_bond_fixed_endpoint_bias_style</b> = 'analytic using max and min 2-4 distance'</dt>
<dt><b>nch_nb_one</b> = 10</dt>
<dt><b>nch_nb</b> = 10</dt>
<dt><b>nch_pre_nb</b> = 1</dt>
<dt><b>nch_tor</b> = 360</dt>
<dt><b>nch_tor_connect</b> = 360</dt>
<dt><b>nch_bend_a</b> = 100</dt>
<dt><b>nch_bend_b</b> = 100</dt>
<dt><b>nch_vib</b> = 1000</dt>
<dt><b>vibrang</b> = 0.85 1.15</dt>
</ul>
</li>
<li>'default autofit gaussian': sets up all of the configurational-bias variables to autofit gaussian settings. This option sets the following
variables for all molecule types in the system. For more information about these variables see the explicit setting for this variable).
<ul>
<dt><b>cbmc_bond_generation</b> = 'autofit gaussian'</dt>
<dt><b>bond_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>cbmc_bend_generation</b> = 'autofit gaussian'</dt>
<dt><b>bend_a_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>bend_b_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>cbmc_dihedral_generation</b> = 'autofit gaussian'</dt>
<dt><b>dihedral_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>cbmc_nb_one_generation</b> = 'uniform'</dt>
<dt><b>two_bond_fixed_endpoint_bias_style</b> = 'autofit gaussian'</dt>
<dt><b>two_bond_bias_sdev_multiplier</b> = 1.0d0</dt>
<dt><b>two_bond_bias_vibrange</b> = 0.5d0 1.5d0</dt>
<dt><b>three_bond_fixed_endpoint_bias_style</b> = 'autofit gaussian using max and min 2-4 distance'</dt>
<dt><b>three_bond_bias_sdev_multipler</b> = 1.0d0</dt>
<dt><b>nch_nb_one</b> = 10</dt>
<dt><b>nch_nb</b> = 10</dt>
<dt>if <b>cbmc_formulation</b> = 'Martin and Siepmann 1999 + Martin and Thompson 2004' then
<ul>
<dt><b>nch_pre_nb</b> = 1</dt>
<dt><b>nch_tor</b> = 10</dt>
<dt><b>nch_tor_connect</b> = 10</dt>
</ul>
</dt>
<dt>else if <b>cbmc_formulation</b> = 'Martin and Frischknecht 2006' then
<ul>
<dt><b>nch_pre_nb</b> = 10</dt>
<dt><b>nch_tor</b> = 1</dt>
<dt><b>nch_tor_connect</b> = 1</dt>
</ul>
</dt>
<dt><b>nch_bend_a</b> = 1</dt>
<dt><b>nch_bend_b</b> = 1</dt>
<dt><b>nch_vib</b> = 1</dt>
</ul>
</li>
<li>'explicit': All of the configurational-bias options are explicitly required. When using this
option you also need to include the following variables.
<ul>
<dt><a name="cbmc_nb_one_generation"><b>cbmc_nb_one_generation (character*30 array)
[one line for each simulation box and each line contains one value for each molecule type]</b></a>
<ul>
<li>'uniform' : the trial coordinates of first atom inserted into this simulation box are generated uniformly</li>
<li>'energy bias' : the trial coordinates of the first atom inserted into this simulation box are generated by selecting a subvolume according to
the Boltzmann weighted energy of a test atom in the center of each subvolume, averaged over all possible insertion atoms in the mapped molecule.
Once a subvolume is selected then a position in that subvolume is generated uniformly. This biasing scheme was first used by
<a href="../references.html#snurr_et_al_1993">Snurr <i>et al.</i> 1993</a>. Note that the energy map used in practice is a linear combination
of the Boltzmann weighted map described above (0.99 of the fraction) with a random selection of any subcube in the box (0.01 of the fraction) to
make sure that the generation probability is strictly positive in all subcubes. The insertion energies are computed using the initial positions
of all molecules in simulation box 1. If you are using this to help with insertions in a porous solid then you may want to only compute this
for the empty porous solid and use the restart of that map in future simulations.
When using this option you need the following variables.
<ul>
<dt><a name="mapmolty"><b>mapmolty (integer)</b></a>
<ul>
<li>The molecule type to use as the insertion probe for determining the energy biasing weights.</li>
</ul>
</dt>
<dt><a name="lcreatemap"><b>lcreatemap (logical)</b></a>
<ul>
<li>.true. if you wish to create a new towhee_map file. This file contains information about the energy profile of the porous molecule.
When using this setting you must also include the following additional variables
<ul>
<dt><a name="cubexyz"><b>cubex,cubey,cubez (integer)</b></a>
<ul>
The number of cubelets you want to have in each direction of the box. Each dimension of the box is divided by the corresponding cube*
value and for each cube an energy value is computed. This value is then used for biasing insertion/deletion moves. cubex*cubey*cubez
mustbe less than or equal to <a href="../code/code_manual.html#MAXCUBE">MAXCUBE</a></b>
</ul>
</dt>
</ul>
</li>
<li>.false. if you want to use a previously generated map in the towhee_map file. That file must have been generated using version 5.2.4 or
later as there was a different, and problematic, format prior to that version.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="nch_nb_one"><b>nch_nb_one (integer) [one value for each molecule type]</b></a>
<ul>
<li>The number of trial positions that are sampled for the first atom inserted during a
<a href="../algorithm/cbmc.html">configurational-bias</a> or rotational-bias molecule exchange move
(see pm2boxrbswap, pm2boxcbswap, and pm1boxcbswap).
</li>
</ul>
</dt>
<dt><a name="nch_nb"><b>nch_nb (integer) [one value for each molecule type]</b></a>
<ul>
<li>The number of trial positions that are sampled for all atoms except for the first atom inserted during a
<a href="../algorithm/cbmc.html">configurational-bias</a> molecule exchange move (see pm2boxcbswap and pm1boxcbswap). This is used for all atoms
in a <a href="../algorithm/cbmc.html">configurational-bias</a> regrowth move.
</li>
</ul>
</dt>
<dt><a name="nch_pre_nb"><b>nch_pre_nb (integer) [one value for each molecule type]</b></a>
<dt>This variable is only required when the <b>cbmc_formulation</b> is 'Martin and Frischknecht 2006'</dt>
<ul>
<li>The number of trials for a selection procedure that takes place after the dihedral selection, but before the nonbond selection when using a
<b>cbmc_formulation</b> of 'Martin and Frischknecht 2006'.
</li>
</ul>
</dt>
<dt><a name="cbmc_dihedral_generation"><b>cbmc_dihedral_generation (character*30)</b></a>
<ul>
<li>'ideal': dihedral trials are generated according to the ideal distribution. For dihedrals that means trials are generation uniformly on
(-Pi, Pi).
</li>
<li>'global gaussian': dihedral trials are generated according a series of gaussian distributions that are a function of the <b>bondpatt</b>
on the central two atoms. This series is hard coded into Towhee and details can be found by looking in the getcbdihed.F subroutine. This
gaussian bias is then removed in the acceptance rule. When using this option you must also include the following variable.
<ul>
<dt><a name="sdevtor"><b>sdevtor (double precision)</b></a>
<ul>
The standard deviation (with units of degrees) that is used for each of the gaussian distributions for the dihedral angles. For best results
this number should be set to the observed distribution computed in the <a href="../utils/analyse_movie.html">analyse_movie</a> utility.
This number must be positive and a default value of 20.0 is suggested.
</ul>
</dt>
</ul>
</li>
<li>'autofit gaussian': dihedral trials are generated according to a series of gaussian distributions that are individually fit to the Boltzmann
factor as a function of dihedral angle for each individual dihedral in the system. This fit is performed automatically at the start of each
simulation using the equilibrium bond lengths and bending angles. This bias is then removed in the acceptance rule. When using this option
you must also include the following variable.
<ul>
<dt><a name="dihedral_sdev_multiplier"><b>dihedral_sdev_multiplier (double precision)</b></a>
<ul>
The factor that is multiplied by the observed gaussian standard deviation for each peak in the automatic dihedral fit in order to create the
standard deviations that are used to generate the dihedrals during the simulation. This number must be positive and a default
value of 1.0 is suggested.
</ul>
</dt>
</ul>
</li>
<li>'ideal + autofit gaussian': dihedral trials are generated according to a linear combination of the ideal distribution (uniform) and a series
of gaussian distributions that are individually fit to the Boltzmann factor as a function of dihedral angle for each individual dihedral in the
system. This fit is performed automatically at the start of each simulation using the equilibrium bond lengths and bending angles. This bias
is then removed in the acceptance rule. When using this option you must also include the following variables.
<ul>
<dt><a name="dihedral_peak_weight_style"><b>dihedral_peak_weight_style (character*30)</b></a>
<ul>
<li>'uniform': each peak is selected with the same (uniform) probability.</li>
<li>'isolated Boltzmann': the peaks are selected with a probability proportional to the sum of the Boltzmann weight computed during the
automatic fitting process.
</li>
</ul>
</dt>
<dt><a name="dihedral_sdev_multiplier"><b>dihedral_sdev_multiplier (double precision)</b></a>
<ul>
The factor that is multiplied by the observed gaussian standard deviation for each peak in the automatic dihedral fit in order to create the
standard deviations that are used to generate the dihedrals during the simulation. This number must be positive and a default
value of 1.0 is suggested.
</ul>
</dt>
<dt><a name="dihedral_ideal_fraction"><b>dihedral_ideal_fraction (double precision)</b></a>
<ul>
The fraction of dihedral trials that are generated using the ideal distribution. The remainder of the trials are generated using the autofit
gaussians. This number must be in the range [0.0,1.0] inclusive.
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="nch_tor"><b>nch_tor (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of trial dihedral angles that are sampled during <a href="../algorithm/cbmc.html">configurational-bias</a> moves. The value must
be positive.
</li>
</ul>
</dt>
<dt><a name="nch_tor_connect"><b>nch_tor_connect (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of trial dihedral angles that are sampled during <a href="../algorithm/cbmc.html">configurational-bias</a> moves when we have
grown the molecule such that we need to connect back up with atoms that already exist. This is needed in order to regrow cyclic molecules,
and to regrow the interiors of large molecules.
The value must be positive.
</li>
</ul>
</dt>
<dt><a name="cbmc_bend_generation"><b>cbmc_bend_generation (character*30)</b></a>
<ul>
<li>'ideal': bending trials are generated according to the ideal distribution. This is the Sine distribution for bending angle type A and uniform
on (-Pi, Pi) for bending angle type B.
</li>
<li>'global gaussian': bending trials are generated according to gaussian distributions. Bending A trials are generated according to a single
gaussian with a mean set to the equilibrium bending angle and a standard deviation set to <b>sdevbena</b>. Bending B trials are generated
according to one or more gaussian distributions with means set based upon the <b>bondpatt</b> of the central atom and a standard deviation
set to <b>setbenb</b>. For more details on the bending B distribution see the getcbangle.F subroutine.
When using this option you must also include the following variables.
<ul>
<dt><a name="sdevbena"><b>sdevbena (double precision)</b></a>
<ul>
The standard deviation to use when generating the part A bending trials (units of degrees). Must be positive, and it is best to set to the
observed distribution of the angles as measured by the <a href="../utils/analyse_movie.html">analyse_movie</a> utility.
</ul>
</dt>
<dt><a name="sdevbenb"><b>sdevbenb (double precision)</b></a>
<ul>
The standard deviation to use when generating the part B bending trials (units of degrees). Must be positive, and it is best to set to the
observed distribution of the angles as measured by the <a href="../utils/analyse_movie.html">analyse_movie</a> utility.
</ul>
</dt>
</ul>
</li>
<li>'autofit gaussian': bending trials are generated according to gaussian distributions. Bending A trials are generated according to a single
gaussian with a mean and standard deviation fit to Sin(theta)*exp(-beta U<sub>bend</sub>). The standard deviation used to generate trials is
a product of the observed distribution standard deviation times <b>bend_a_sdev_multiplier</b>. Bending B trials are generated according to one
or more gaussian distributions with means fitted to exp(-beta u<sub>bend</sub>) for rotating the angles about a cone (with everything else set
to the equilibrium bond lengths and bending angles). The observed standard deviation from this fit is multiplied by
<b>bend_b_sdev_multiplier</b> to get the standard deviation used to generate bending B angles during the simulation. This bias is removed in
the acceptance rules. When using this option you must also include the following variables.
<ul>
<dt><a name="bend_a_sdev_multiplier"><b>bend_a_sdev_multiplier (double precision)</b></a>
<ul>
This value is multiplied by the observed standard deviation from performing the fit in order to create the standard deviation that is used
to generate bending A trials during the simulation. This value must be positive and the currently suggested value is 1.0.
</ul>
</dt>
</ul>
<ul>
<dt><a name="bend_b_sdev_multiplier"><b>bend_b_sdev_multiplier (double precision)</b></a>
<ul>
This value is multiplied by the observed standard deviation from performing the fit in order to create the standard deviation that is used
to generate bending B trials during the simulation. This value must be positive and the currently suggested value is 1.0.
</ul>
</dt>
</ul>
</li>
<li>'ideal + autofit gaussian': bending trials are generated according to a linear combination of the ideal distributions (sine for bend A,
uniform for bend B) and the autofit gaussian distributions. Gaussian bending A trials are generated according to a single gaussian with a mean
and standard deviation fit to Sin(theta)*exp(-beta U<sub>bend</sub>). The standard deviation used to generate trials is a product of the
observed distribution standard deviation times <b>bend_a_sdev_multiplier</b>. Gaussian bending B trials are generated according to one or more
gaussian distributions with means fitted to exp(-beta u<sub>bend</sub>) for rotating the angles about a cone (with everything else set to the
equilibrium bond lengths and bending angles). The observed standard deviation from this fit is multiplied by <b>bend_b_sdev_multiplier</b>
to get the standard deviation used to generate bending B angles during the simulation. This bias is removed in the acceptance rules. When using
this option you must also include the following variables.
<ul>
<dt><a name="bend_a_sdev_multiplier"><b>bend_a_sdev_multiplier (double precision)</b></a>
<ul>
This value is multiplied by the observed standard deviation from performing the fit in order to create the standard deviation that is used to
generate bending A trials during the simulation. This value must be positive and the currently suggested value is 1.0.
</ul>
</dt>
<dt><a name="bend_b_sdev_multiplier"><b>bend_b_sdev_multiplier (double precision)</b></a>
<ul>
This value is multiplied by the observed standard deviation from performing the fit in order to create the standard deviation that is used to
generate bending B trials during the simulation. This value must be positive and the currently suggested value is 1.0.
</ul>
</dt>
<dt><a name="bend_a_ideal_fraction"><b>bend_a_ideal_fraction (double precision)</b></a>
<ul>
The fraction of bending A trials that are generated using the ideal distribution of Sin(theta). The remainder of the trials are generated
using the autofit gaussians. This value must be in the range [0.0,1.0] inclusive.
</ul>
</dt>
<dt><a name="bend_b_ideal_fraction"><b>bend_b_ideal_fraction (double precision)</b></a>
<ul>
The fraction of bending B trials that are generated using the ideal distribution of uniform on (-Pi,Pi). The remainder of the trials are
generated using the autofit gaussians. This value must be in the range [0.0,1.0] inclusive.
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="nch_bend_a"><b>nch_bend_a (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of trial angles that are sampled during <a href="../algorithm/cbmc.html">configurational-bias</a> moves when we are selecting the
iugrow-iufrom-iuprev angle. This value must be positive. Currently suggested values are in the range of 100 to 1000 when using
<b>cbmc_bend_generation</b> style 'ideal' and in the range from 1 to 10 when using <b>cbmc_bend_generation</b> styles 'global gaussian'
or 'autofit gaussian'.
</li>
</ul>
</dt>
<dt><a name="nch_bend_b"><b>nch_bend_b (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of trial angles that are sampled during <a href="../algorithm/cbmc.html">configurational-bias</a> moves when we are selecting the
rotation about a cone of one of the iugrow angles relative to the others. This value must be positive. Currently suggested values are in
the range of 100 to 1000 when using <b>cbmc_bend_generation</b> style 'ideal' and in the range from 1 to 10 when using
<b>cbmc_bend_generation</b> styles 'global gaussian' or 'autofit gaussian'.
</li>
</ul>
</dt>
<dt><a name="cbmc_bond_generation"><b>cbmc_bond_generation (character*30)</b></a>
<ul>
<li>'r^2 with bounds': Generate trial bond lengths according to a bounded r<sup>2</sup> probability distribution within the ranges set by the
<b>vibrang</b> variable. This distribution is proportional to the true distribution, but has a limited sampling range while the true
distribution is of infinite extent When using this option you also need to include the following variable.
<ul>
<dt><a name="vibrang"><b>vibrang (double precision, double precision)</b></a>
<ul>
The range of bond lengths to sample via <a href="../algorithm/cbmc.html">configurational-bias</a> Monte Carlo. The range is expressed as a
fraction of the equilibrium bond length for the lower bound and the upper bound. Currently suggested values are 0.85 and 1.15.
</ul>
</dt>
</ul>
</li>
<li>'global gaussian': Generate trial bond lengths according to a gaussian distribution with a mean set to the equilibrium bond length and a
standard deviation specified as <b>sdevvib</b>. When using this option you must also include the following variable.
<ul>
<dt><a name="sdevvib"><b>sdevvib (double precision)</b></a>
<ul>
The standard deviation of a gaussian distribution that is used to sample bond lengths during a
<a href="../algorithm/cbmc.html">configurational-bias</a> regrowth for a <b>cbmc_bond_generation</b> style of 'global gaussian'.
Units are Angstroms. For best results perform a short simulation of single-atom translation moves, analyse that data using the
<a href="../utils/analyse_movie.html">analyse_movie</a> utility, and set this value to the observed standard deviations in the bond length
distribution.
</ul>
</dt>
</ul>
</li>
<li>'autofit gaussian': Generate trial bond lengths according to a gaussian distribution with a mean and standard deviation fitted to
r<sup>2</sup> exp<sup>(-beta U<sub>bond</sub>)</sup>. When using this option you also need to include the following variable.
<ul>
<dt><a name="bond_sdev_multiplier"><b>bond_sdev_multiplier (double precision)</b></a>
<ul>
This value is multiplied by the observed standard deviation of the r<sup>2</sup> exp<sup>(-beta U<sub>bond</sub>)</sup> distribution in order
to determine the standard deviation used to generate bond trials. This value must be positive. The currently suggested value is 1.0.
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="nch_vib"><b>nch_vib (integer) [one value for each molecule type]</b></a>
<ul>
<li> The number of trial bond lengths that are sampled during a <a href="../algorithm/cbmc.html">configurational-bias</a> move. This value must be
positive. Currently suggested values are 1000 trials for <b>cbmc_bond_generation</b> style 'r^2 with bounds' and a value in the range
of 1 to 10 for <b>cbmc_bond_generation</b> styles 'global gaussian' and 'autofit gaussian'.
</li>
</ul>
</dt>
<dt><a name="two_bond_fixed_endpoint_bias_style"><b>two_bond_fixed_endpoint_bias_style (character*50)</b></a>
<ul>
<li>'none': No additional biasing is utilized during a configurational-bias move step that involves the growth of a new atom that is separated
from an already existing atom by two bonds where the atom between those two bonds does not currently exist.
</li>
<li>'analytic Boltzmann using angles': Additional biasing is utilized during a configurational-bias move step that involves the growth of a new
atom that is separated from an already existing atom by two bonds where the atom between those two bonds does not currently exist. The biasing
has the following form where i is the atom being grown, k is an atom that already exists, and j is an atom that is bonded to i and j, but
has not yet been grown.
<dt>p<sub>bias</sub>(r<sub>ik</sub>) = Min[minbias,p<sub>aBua</sub>].</dt>
<dt>p<sub>aBua</sub>
<ul>
= p<sub>angle</sub> for r<sub>ik</sub> < r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup>
</ul>
<ul>
= p<sub>bond</sub> for r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup> < r<sub>ik</sub>
</ul>
</dt>
<dt>p<sub>angle</sub> = Exp[- &beta u<sub>angle</sub>( &theta<sub>ijk</sub> ) ]
<ul>
where &theta<sub>ijk</sub> is computed from the trial r<sub>ik</sub> distance and the equilibrium bond lengths of the two missing bonds
(r<sub>ij</sub><sup>0</sup> and r<sub>jk</sub><sup>0</sup>).
</ul>
</dt>
<dt>p<sub>bond</sub> = Exp[- &beta ( u<sub>angle</sub>( &theta<sub>ijk</sub> ) + u<sub>bond</sub>( r<sub>ij</sub> )
+ u<sub>bond</sub>( r<sub>jk</sub> ) ) ]
<ul>
where &theta<sub>ijk</sub> = &pi, r<sub>ij</sub> = r<sub>ij</sub><sup>0</sup> * r<sub>ik</sub>
/ ( r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup> ),
and
r<sub>jk</sub> = r<sub>jk</sub><sup>0</sup> * r<sub>ik</sub> / ( r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup> ),
</ul>
</dt>
minbias is a minimum value set in the code in order to avoid division by zero. This is set in the febias.F subroutine and currently has a
value of 1.0d-40.
</li>
<li>'analytic Boltzmann dihedral energy sum': Additional biasing is utilized during a configurational-bias move step that involves the growth of
a new atom that is separated from an already existing atom by two bonds where the atom between those two bonds does not currently exist.
The biasing has the following form where i is the atom being grown, h is an atom that already exists and is the atom from which i is being grown
this step, k is an atom that already exists, and j is an atom that is bonded to i and j, but has not yet been grown.
<dt>p<sub>bias</sub>(r<sub>ij</sub>) = Min[minbias,p<sub>aBdes</sub>].</dt>
<dt>p<sub>aBdes</sub>
<ul>
= p<sub>dihedral</sub> for r<sub>ik</sub> < r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup>
</ul>
<ul>
= minbias for r<sub>ij</sub><sup>0</sup> + r<sub>jk</sub><sup>0</sup> < r<sub>ik</sub>
</ul>
</dt>
<dt>p<sub>dihedral</sub> = Exp[- &beta (u<sub>dihedral</sub>(&phi<sub>hijk</sub>(1)) + u<sub>dihedral</sub>(&phi<sub>hijk</sub>(2)) )]
<ul>
where &phi<sub>hijk</sub>(1) and &phi<sub>hijk</sub>(2) are the two possible solutions for that dihedral given the following constraints,
<ul>
<dt>r<sub>ij</sub> = r<sub>ij</sub><sup>0</sup></dt>
<dt>r<sub>jk</sub> = r<sub>jk</sub><sup>0</sup></dt>
<dt>&theta<sub>hij</sub> = &theta<sub>hij</sub><sup>0</sup></dt>
</ul>
</ul>
</dt>
</li>
<li>'autofit gaussian': Additional biasing is utilized during a configurational-bias move step that involves the growth of a new atom that is
separated from an already existing atom by two bonds, where the atom between those two bonds does not currently exist. The biasing is a
gaussian distribution that is fit to the following distribution where i is the atom being grown, k is an atom that already exists, and j is an
atom that is bonded to i and j, but has not yet been grown.
<dt>p<sub>ag</sub> = r<sub>ij</sub><sup>2</sup> r<sub>jk</sub><sup>2</sup> &theta<sub>ijk</sub>
Exp[-&beta ( u<sub>bond</sub>(r<sub>ij</sub>) + u<sub>bond</sub>(r<sub>jk</sub>) + u<sub>angle</sub>(&theta<sub>ijk</sub>) )]
</dt>
<dt>where this distribution is computed at the beginning of the simulation and then the mean and standard deviations are stored for use during
the configurational-bias growth procedure. When using this option you must also include the following additional variables.
<ul>
<dt><a name="two_bond_bias_sdev_multiplier"><b>two_bond_bias_sdev_multiplier (double precision)</b></a>
<ul>
<li>This value is multiplied by the standard deviation determined from the fit in order to get the standard deviation that is used during
the simulation. Must be positive.
</li>
</ul>
</dt>
<dt><a name="two_bond_bias_vibrange"><b>two_bond_bias_vibrange (double precision array) </b></a>
<ul>
<li>These are the lower and upper bounds of sampling for the r<sub>ij</sub> and r<sub>jk</sub> bond lengths that are varied at the start of
the simulation in order to determine the gaussian fit parameters. They are in units relative to the equilibrium bond lengths. Suggested
default values are 0.5 and 1.5.
</li>
</ul>
</dt>
</ul>
</dt>
</li>
<li>'self adapting gaussian using 1-3 distance': Additional biasing is utilized during a configurational-bias move step that involves the growth
of a new atom that is separated from an already existing atom by two bonds, where the atom between those two bonds does not currently exist.
The biasing is a gaussian distribution based upon the distance between the atom being grown and the target atom that is two bonds away and
already exists. This gaussian distribution is self adapted during the course of a simulation so that it represents the observed 1-3 distance
distribution. When using this option you must also include the following additional variables.
<ul>
<dt><a name="two_bond_bias_sdev_multiplier"><b>two_bond_bias_sdev_multiplier (double precision)</b></a>
<ul>
<li>This value is multiplied by the standard deviation determined from the fit in order to get the standard deviation that is used during
the simulation. Must be positive.
</li>
</ul>
</dt>
<dt><a name="two_bond_bias_initial_value"><b>two_bond_bias_initial_value (character*50)</b></a>
<ul>
<li>'file': the initial distribution is read from the 'towhee_safe_initial' file in the local directory. This file is generally copied from
the 'towhee_safe_final' file that is produced at the end of a simulation that employed this <b>two_bond_fixed_endpoint_bias_style</b>.
</li>
<li>'autofit gaussian': the initial distribution is generated by automatically fitting a gaussian to a sampling of the r<sub>ik</sub>
distance. This option is recommended when starting a new simulation where there is no appropriate 'towhee_safe_initial' file available.
</li>
</ul>
</dt>
<dt><a name="two_bond_bias_compute_frequency"><b>two_bond_bias_compute_frequency (integer) </b></a>
<ul>
<li>Statistics on the two bond bias distributions are taken from the simulation with a step frequency equal to this value. These statistics
are then periodically used to update the distributions, as described in the
<a href="#two_bond_bias_update_frequency"><b>two_bond_bias_update_frequency</b></a> section. Set this value to 0 if you wish to disable
the periodic computation of these distributions.
</li>
</ul>
</dt>
<dt><a name="two_bond_bias_update_frequency"><b>two_bond_bias_update_frequency (integer)</b></a>
<ul>
<li>The distributions used to perform the two bond biasing are updated with this step frequency. The updates combine the distributions
computed with a frequency controlled by the <a href="#two_bond_bias_compute_frequency"><b>two_bond_bias_compute_frequency</b></a> variable
with the previous version of the two bond biasing potentials to create the new two bond biasing potential. Set to 0 to disable this update.
</li>
</ul>
</dt>
<dt><a name="two_bond_bias_old_fraction"><b>two_bond_bias_old_fraction (double precision)</b></a>
<ul>
<li>This factor determines the linear combination of the old distribution, and the observed distribution, to determine the new two bond bias
distribution. This number must be in the range [0.0,1.0] inclusive. Setting this value to 0.0 would completely replace the old
distribution with the new distribution, while a setting of 0.5 would combine the old and observed distributions equally in order to compute
the new distribution.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<dt><a name="three_bond_fixed_endpoint_bias_style"><b>three_bond_fixed_endpoint_bias_style (character*50)</b></a>
<ul>
<li>'none': No additional biasing is utilized during a configurational-bias move step that involves the growth of a new atom that is separated
from an already existing atom by three bonds where the atoms between those three bonds do not currently exist.
</li>
<li>'analytic using max and min 2-4 distance': Additional biasing is utilized during a configurational-bias move step that involves the growth
of a new atom that is separated from an already existing atom by three bonds where the atoms between those three bonds do not currently exist.
The biasing has the following form where i is the atom being grown, h is an atom that already exists and is the atom from which i is being grown
this step, l is an atom that already exists, and j and k are atoms that have not yet been regrown and bridge the gap between atoms i and l.
The biasing with this option depends upon the minimum (r<sub>jl</sub><sup>min</sup>) and maximum (r<sub>jl</sub><sup>max</sup>) projected
distances between the j and l atoms given the constraints that r<sub>ij</sub> and &theta<sub>hij</sub> are set to their equilibrium
values (r<sub>ij</sub><sup>0</sup> and &theta<sub>hij</sub><sup>0</sup>). These minimum and maximum distances are then compared with the
equilibrium distance between the j and l atoms (r<sub>jl</sub><sup>eq</sup>). This equilibrium distance is computed by setting
r<sub>jk</sub> = r<sub>jk</sub><sup>0</sup>, r<sub>kl</sub> = r<sub>kl</sub><sup>0</sup>,
and &theta<sub>jkl</sub> = &theta<sub>jkl</sub><sup>0</sup>). The biasing value is computed as follows.
<dt>p<sub>aumam24d</sub>
<ul>
= p<sub>stretch</sub> for r<sub>jl</sub><sup>eq</sup> < r<sub>jl</sub><sup>min</sup>
</ul>
<ul>
= 1.0 for r<sub>jl</sub><sup>min</sup> < r<sub>jl</sub><sup>eq</sup> < r<sub>jl</sub><sup>max</sup>
</ul>
<ul>
= p<sub>compress</sub> for r<sub>jl</sub><sup>max</sup> < r<sub>jl</sub><sup>eq</sup></dt>
</ul>
</dt>
<dt>p<sub>stretch</sub>
<ul>
= Exp[- &beta u<sub>angle</sub>(&theta<sub>jkl</sub>)] where &theta<sub>jkl</sub> is computed given the constraints of
r<sub>jk</sub><sup>0</sup>, r<sub>kl</sub><sup>0</sup>, and r<sub>jl</sub><sup>min</sup> for r<sub>jl</sub><sup>min</sup>
& lt; r<sub>jk</sub><sup>0</sup> + r<sub>kl</sub><sup>0</sup>.
</ul>
<ul>
= Exp[- &beta ( u<sub>angle</sub>(&theta<sub>jkl</sub>) + u<sub>bond</sub>(r<sub>jk</sub>)
+ u<sub>bond</sub>(r<sub>kl</sub>) )] where &theta<sub>jkl</sub> = &pi,
r<sub>jk</sub> = r<sub>jk</sub><sup>0</sup> * r<sub>jl</sub><sup>min</sup>
/ ( r<sub>jk</sub><sup>0</sup> + r<sub>kl</sub><sup>0</sup> ),
and
r<sub>kl</sub> = r<sub>kl</sub><sup>0</sup> * r<sub>jl</sub><sup>min</sup>
/ ( r<sub>jk</sub><sup>0</sup> + r<sub>kl</sub><sup>0</sup> )
for r<sub>jk</sub><sup>0</sup> + r<sub>kl</sub><sup>0</sup> < r<sub>jl</sub><sup>min</sup>.
</ul>
</dt>
<dt>p<sub>compress</sub> = Exp[- &beta u<sub>angle</sub>(&theta<sub>jkl</sub>) ]
<ul>
where &theta<sub>jkl</sub> is computed using the constraints r<sub>jk</sub><sup>0</sup>, r<sub>kl</sub><sup>0</sup>,
and r<sub>jl</sub><sup>max</sup>.
</ul>
</dt>
</li>
<li>'autofit gaussian using max and min 2-4 distance': Additional biasing is utilized during a configurational-bias move step that involves
the growth of a new atom that is separated from an already existing atom by three bonds where the atoms between those three bonds do not
currently exist. The biasing has the following form where i is the atom being grown, h is an atom that already exists and is the atom from
which i is being grown this step, l is an atom that already exists, and j and k are atoms that have not yet been regrown and bridge
the gap between atoms i and l. The biasing with this option depends upon the minimum (r<sub>jl</sub><sup>min</sup>) and
maximum (r<sub>jl</sub><sup>max</sup>) projected distances between the j and l atoms given the constraints that r<sub>ij</sub>
and &theta<sub>hij</sub> are set to their equilibrium values (r<sub>ij</sub><sup>0</sup> and &theta<sub>hij</sub><sup>0</sup>).
These extrema are then combined with the 'autofit gaussian' biasing described for the
<a href="#two_bond_fixed_endpoint_bias_style"><b>two_bond_fixed_endpoint_bias_style</b></a> option. The bias probability is set to the
integrated probability of that autofit gaussian on the limits between r<sub>jl</sub><sup>min</sup> and r<sub>jl</sub><sup>max</sup>.
When using this option you also need to include the following variable.
<ul>
<dt><a name="three_bond_bias_sdev_multiplier"><b>three_bond_bias_sdev_multiplier</b></a>
<ul>
<li>This value is multiplied by the standard deviation determined from the fit in order to get the standard deviation that is used
during the simulation. Must be positive.
</li>
</ul>
</dt>
</ul>
</li>
<li>'self adapting gaussian using 1-4 distance': Additional biasing is utilized during a configurational-bias move step that involves the
growth of a new atom that is separated from an already existing atom by three bonds where the atoms between those three bonds do not
currently exist. The biasing has the following form where i is the atom being grown, h is an atom that already exists and is the atom from
which i is being grown this step, l is an atom that already exists, and j and k are atoms that have not yet been regrown and bridge
the gap between atoms i and l. The biasing is a gaussian that depends only upon the r<sub>il</sub> distance. This gaussian distribution
can be set to self-adapt during the course of the simulation so that the biasing probability reflects the observed probability for the
r<sub>il</sub> distances. When using this option you also need to include the following variables.
<ul>
<dt><a name="three_bond_bias_sdev_multiplier"><b>three_bond_bias_sdev_multiplier</b></a>
<ul>
<li>This value is multiplied by the standard deviation determined from the fit in order to get the standard deviation that is used
during the simulation. Must be positive.
</li>
</ul>
</dt>
<dt><a name="three_bond_bias_initial_value"><b>three_bond_bias_initial_value (character*50)</b></a>
<ul>
<li>'file': the initial distribution is read from the 'towhee_safe_initial' file in the local directory. This file is copied from
the 'towhee_safe_final' file that is generated at the end of a simulation run that employed the appropriate
<a href="#three_bond_fixed_endpoint_bias_style"><b>three_bond_fixed_endpoint_bias_style</b></a>.
</li>
<li>'autofit gaussian': the initial distribution is automatically fit to the Boltzmann weight as a function of r<sub>il</sub> distances
using the equilibrium r<sub>ij</sub>, r<sub>jk</sub>, and r<sub>kl</sub> bond lengths and the equilibrium &theta<sub>ijk</sub>
and &theta<sub>jkl</sub> angles. This option is recommended for the initial simulation when no appropriate 'towhee_safe_initial' file
exists.
</li>
</ul>
</dt>
<dt><a name="three_bond_bias_compute_frequency"><b>three_bond_bias_compute_frequency (integer) </b></a>
<ul>
<li>Statistics on the three bond bias distributions are taken from the simulation with a step frequency equal to this value. These
statistics are then periodically used to update the distributions, as described in the
<a href="#three_bond_bias_update_frequency"><b>three_bond_bias_update_frequency</b></a>
section. Set this value to 0 if you wish to disable the periodic computation of these distributions.
</li>
</ul>
</dt>
<dt><a name="three_bond_bias_update_frequency"><b>three_bond_bias_update_frequency (integer)</b></a>
<ul>
<li>The distributions used to perform the three bond biasing are updated with this step frequency. The updates combined the distributions
computed with a frequency controlled by the <a href="#three_bond_bias_compute_frequency"><b>three_bond_bias_compute_frequency</b></a>
variable with the previous version of the three bond biasing potentials to create the new three bond biasing potential.
Set to 0 to disable this update.
</li>
</ul>
</dt>
<dt><a name="three_bond_bias_old_fraction"><b>three_bond_bias_old_fraction (double precision)</b></a>
<ul>
<li>This factor determines the linear combination of the old distribution, and the observed distribution, to determine the new three bond
bias distribution. This number must be in the range [0.0,1.0] inclusive. Setting this value to 0.0 would completely replace the old
distribution with the new distribution, while a setting of 0.5 would combine the old and observed distributions equally in order to
compute the new distribution.
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
</ul>
</li>
</ul>
</dt>
<p> </p>
<dt>The final section of towhee_input contains the information that is used to construct the forcefield for the molecule types in the
system. The choice of inpstyle determines which other variables are required to describe the molecule. Click on the appropriate link for each
inpstyle to learn about the remaining variables that are required for each case.
</dt>
<dt><a name="input_style"><b>input_style (character*50)</b></a>
<ul>
<li>'explicit' : <a href="../inpstyle/inpstyle_0.html">Explicit declaration of all terms</a> (formerly <b>inpstyle</b> 0)</li>
<li>'polypeptide builder' : <a href="../inpstyle/inpstyle_1.html">Polypeptide builder</a> (formerly <b>inpstyle</b> 1)</li>
<li>'basic connectivity map' : <a href="../inpstyle/inpstyle_2.html">Basic Atom-based connectivity map</a> (formerly <b>inpstyle</b> 2)</li>
<li>'nucleic acid builder' : <a href="../inpstyle/inpstyle_3.html">Nucleic acid builder</a> (formerly <b>inpstyle</b> 3)</li>
<li>'nanotube builder' : <a href="../inpstyle/inpstyle_4.html">Nanotube builder</a> (formerly <b>inpstyle</b> 4)</li>
<li>'atomic' <a href="../inpstyle/inpstyle_5.html">Atomic only: typically for use with external quantum energy calcaultions</a>
(formerly <b>inpstyle</b> 5)
</li>
<li>'advanced connectivity map' : <a href="../inpstyle/inpstyle_6.html">Advanced Atom-based connectivity map</a></li>
</ul>
</dt>
</ul>
<a href="../index.html">Return to the main towhee web page</a>
<p> </p>
</td>
</tr>
</table>
<hr width="715" align="left"></hr>
<i><font size="2">Send comments to:</font></i>
<font size="2"><a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a>
<br></br>
<i>Last updated:</i> <!-- #BeginDate format:Am1 -->August 12, 2011<!-- #EndDate -->
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