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<title>MCCCS Towhee (towhee_input Version 1.3.x)</title>
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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (towhee_input Version 1.3.x)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the variables that are set in the towhee_input file
Version 1.3.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>
</ul>
<b>Variable explanations for towhee_input</b>
<ul>
<dt><b>temperature (double precision)</b>
<ul>
<li> The temperature in Kelvin.</li>
</ul>
<dt><b>pressure (double precision)</b>
<ul>
<li> The external pressure in kPa. This in only used if lnpt = .true.,
but you have to list a value regardless.</li>
</ul>
<dt><b>nchain (integer)</b>
<ul>
<li> The total number of molecules (chains) in the simulation. This
must be less than NMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nmolty (integer)</b>
<ul>
<li> The total number of molecule types in the simulation. This must
be less then or equal to NTMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>moltyp (integer)</b>
<ul>
<li> The number of molecules of each type (listed sequentially on
a single line). These values must add up to the total number of
chains (nchain) specified above.</li>
</ul>
<dt><b>numboxes (integer)</b>
<ul>
<li> The number of simulation boxes in the system. This value must
be less than or equal to MAXBOXES (set in <a href="../code/code_manual.html#preproc">preproc.h</a>). Note that
many of the variables below depend upon numboxes as you will have
to provide information for each box (such as box lengths).</li>
</ul>
<dt><b>lcycles (logical)</b>
<ul>
<li> .true. if nstep is the number of cycles, where a cycle is nchain
Monte Carlo moves (nchain is the number of molecules in the system).</li>
<li> .false. if nstep is the number of Monte Carlo moves.</li>
</ul>
<dt><b>nstep (integer)</b>
<ul>
<li> The number of Monte Carlo steps to perform. If lcycles = .true.
then each step is a cycle, otherwise each step is a single move.</li>
</ul>
<dt><b>iprint (integer)</b>
<ul>
<li> Every iprint Monte Carlo steps information about the system is
output to stdout (fort.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.</li>
</ul>
<dt><b>iblock (integer)</b>
<ul>
<li> The size of the blocks for computing block averages. If you want
this to be meaningful then iblock 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.</li>
</ul>
<dt><b>imovie (integer)</b>
<ul>
<li> The number of steps between 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.</li>
</ul>
<dt><b>ibackup (integer)</b>
<ul>
<li> Every ibackup Monte Carlo steps the code will write 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 ibackup 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.</li>
</ul>
<dt><b>loutpdb (logical)</b>
<ul>
<li> .true. if you wish to output Protein Data Bank (pdb) files for
each simulation box at the end of the run. These files are named
box_xx.pdb where xx is the simulation box number.</li>
<li> .false. if you do not want to output pdb files.</li>
</ul>
<dt><b>loutdft (logical)</b>
<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 Tramonto code for information on what
these files mean.</li>
<li> .false. if you do not want to output dft files.</li>
</ul>
<dt><b>loutlammps (logical)</b>
<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 LAMMPS documentation for more information on how to read
in these files.</li>
<li> .false. if you do not want to output LAMMPS files.</li>
</ul>
<dt><b>iratp (integer)</b>
<ul>
<li> Towhee computes the pressure in each box every iratp Monte Carlo
steps. Be aware that computing the pressure is a fairly expensive
task (especially for large systems) so if you don't really care
about the computed pressure then it will pay to set iratp to a high
value.</li>
</ul>
<dt><b>iratio (integer)</b>
<ul>
<li> The maximum translational (atom and center-of-mass) and rotational
displacements are updated every iratio Monte Carlo steps. They are
adjusted to try and achieve the target acceptance rates (see tatraa,
tatrac, and tarot). 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 I typically set iratio
to do 10 updates during a run.</li>
</ul>
<dt><b>iratv (integer)</b>
<ul>
<li> The maximum volume displacements are updated every iratv Monte
Carlo steps. They are adjusted to try and achieve the target acceptance
rates (see tavol). 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 iratv to do 10 updates
during a run.</li>
</ul>
<dt><b>potentyp (integer)</b>
<ul>
<li> potentyp = 0: 12-6 Lennard-Jones van der Waals potential</li>
<li> potentyp = 1: 9-6 Lennard-Jones van der Waals potential</li>
<li> potentyp = 2: Exponential-6 van der Waals potential</li>
<li> potentyp = 3: Hard Sphere van der Waals potential</li>
<li> potentyp = 4: Exponential plus 12-6 Lennard-Jones van der Waals
potential</li>
</ul>
<dt><b>mixrule (integer)</b>
<ul>
<li> mixrule = 0: Lorentz-Berthelot (arithmetic mean of sigma, geometric
mean of epsilon) mixing rules. Only valid for potentyp = 0.</li>
<li> mixrule = 1: Geometric (geometric mean of sigma and epsilon)
mixing rules. Only valid for potentyp = 0.</li>
<li> mixrule = 2: Compass (sixth order combination of sigma and epsilon)
mixing rules. Only valid for potentyp = 1.</li>
<li> mixrule = 3: Gromos (geometric mean of sigma and epsilon with
some special cases) mixing rules. Only valid for potentyp = 0.</li>
<li> mixrule = 4: Explicit (defined in ffnonbond.F) mixing rules.
Only valid for potentyp = 2 or potentyp = 4.</li>
<li> mixrule = 5: Hard sphere (arithmetic mean of sigmas) mixing rules.
Only valid for potentyp = 3.</li>
</ul>
<dt><b>lshift (logical)</b>
<ul>
<li> .true. if you want the nonbonded van der Waals potential to be
shifted so that it is zero at the cutoff.</li>
<li> .false. if you do not want to shift the nonbonded van der Waals
potential.</li>
</ul>
<dt><b>ltailc (logical)</b>
<ul>
<li> .true. if you want to apply analytical tail corrections for the
portion of the van der Waals potential that is past the cutoff.
Note that you cannot have a shifted potential and tail corrections
at the same time.</li>
<li> .false. if you do not want analytical tail corrections for van
der Waals.</li>
</ul>
<dt><b>rmin (double precision)</b>
<ul>
<li> A hard inner cutoff that can speed computation for Lennard-Jones
systems, and is required to avoid the potential hitting infinity
for exponential repulsion systems which also contain point charges.
This should be set smaller than the smallest radius of any atom.
Generally I set this to 0.5 or 1.0 Angstroms.</li>
</ul>
<dt><b>rcut (double precision)</b>
<ul>
<li> The van der Waals potential cutoff in Angstroms.</li>
</ul>
<dt><b>rcutin (double precision)</b>
<ul>
<li> The inner nonbonded cutoff used in configurational-bias Monte
Carlo moves. This dual-cutoff method can speed configurational-bias
computations by at least a factor of 2, without affecting the acceptance
rate. The inner cutoff is used during the growth procedure, and
the full potential is calculated at the end of the move and everything
is fixed up in the acceptance criteria. I typically set this to
5 Angstroms for noncoulombic simulations, and to 10 Angstroms for
coulombic simulations.</li>
</ul>
<dt><b>lewald (logical)</b>
<ul>
<li> .true. if you want to use an Ewald sum to handle the long range
electrostatics. The Ewald sum is performed in Towhee by computing
all of the minimum image charge interactions using an alpha that
depends upon the x-dimension box length (kalp/boxlx), while the
number of Fourier space vectors is constant (kmax).</li>
<li> .false. if you do want to use an Ewald sum. In this case the
minimum image convention is used to compute all interactions in
order to avoid nasty effects that come from an atom-based cutoff
for electrostatics.</li>
</ul>
<dt><b>kalp (double precision)</b>
<ul>
<li> Value used in the Ewald sum to compute alpha. The minimum value
you can use is 5.0 (and that is also the recommended value) Even
if you are not using the Ewald sum you still have to list this parameter,
though it is not used.</li>
</ul>
<dt><b>kmax (integer)</b>
<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 VECTORMAX
(see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>dielect (double precision)</b>
<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 the dielectric constant to represent
the missing solvent.</li>
</ul>
<dt><b>nhrdfld (integer)</b>
<ul>
<li> Number of hard walls you wish to include in the simulation. As
this is not typically used, it has a slightly different input style
from normal. If nhrdfld = 0 then none of the hrd* variables are
required in the input file. Otherwise for next nhrdfld lines each
line should contain the values for hrdbox(ifield), hrdxyz(ifield),
hrdcen(ifield), hrdrad(ifield) where those variables have the following
meanings.</li>
<li><b>hrdbox (integer)</b>
<ul>
<li> This is the number of the simulation box which contains this
hard wall. Must range from 1 to numboxes.</li>
</ul>
</li>
<li><b>hrdxyz (integer)</b>
<ul>
<li> 1: hard wall is perpendicular to the x-axis (in the yz plane)</li>
<li> 2: hard wall is perpendicular to the y-axis (in the xz plane)</li>
<li> 3: hard wall is perpendicular to the z-axis (in the xy plane)</li>
</ul>
</li>
<li><b>hrdcen (double precision)</b>
<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>
</li>
<li><b>hrdrad (double precision)</b>
<ul>
<li> Radius of the hard wall. The wall will exclude all atoms
whose centers are within this radius regardless of the potentyp
or any of the atom parameters. Yes I know this is a strange
way to run a hard wall. The wall is felt through the periodic
boundaries.</li>
</ul>
</li>
</ul>
<dt><b>nljfld (integer)</b>
<ul>
<li> Number of 9-3 Lennard-Jones walls you wish to include in the
simulation. As this is not typically used, it has a slightly different
input style from normal. If nljfld = 0 then none of the ljf* variables
are required in the input file. Otherwise for next nljfld lines
each line should contain the values for ljfbox(ifield), ljfxyz(ifield),
ljfcen(ifield), ljfsig(ifield), ljfeps(ifield) ,ljfcut(ifield),
and ljfdir(ifield) where those variables have the following meanings.</li>
<li><b>ljfbox (integer)</b>
<ul>
<li> This is the number of the simulation box which contains this
Lennard-Jones wall. Must range from 1 to numboxes.</li>
</ul>
</li>
<li><b>ljfxyz (integer)</b>
<ul>
<li> 1: Lennard-Jones wall is perpendicular to the x-axis (in
the yz plane)</li>
<li> 2: Lennard-Jones wall is perpendicular to the y-axis (in
the xz plane)</li>
<li> 3: Lennard-Jones wall is perpendicular to the z-axis (in
the xy plane)</li>
</ul>
</li>
<li><b>ljfcen (double precision)</b>
<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>
</li>
<li><b>ljfsig (double precision)</b>
<ul>
<li> Sigma parameter for the 9-3 Lennard-Jones wall.</li>
</ul>
</li>
<li><b>ljfeps (double precision)</b>
<ul>
<li> Epsilon parameter for the 9-3 Lennard-Jones wall. All atoms
in the system interact with the wall via the potential U = sqrt(2/5)
ljfeps [ (1/5) (ljfsig/r)^9 - (3/2) (ljfsig/r)^3 ] regardless
of the potentyp and parameters of each atom. Yes I know this
is a strange way to run a 9-3 Lennard-Jones wall, but I don't
use it much.</li>
</ul>
</li>
<li><b>ljfcut (double precision)</b>
<ul>
<li> The distance beyond which the wall-atom interactions are
not computed. This potential is cut, not shifted, and never
has tail corrections no matter how lshift and ltailc are set.</li>
</ul>
</li>
<li><b>ljfdir (integer)</b>
<ul>
<li> -1: Atoms only interact with the "left" face of this wall.
This extends through the periodic boundary.</li>
<li> 1: Atoms only interact with the "right" face of this wall.
This extends through the periodic boundary.</li>
</ul>
</li>
</ul>
<dt><b>linit (logical)</b>
<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><b>initstyle (integer)</b>
<ul>
One line for each simulation box in the system. Each line contains
a value for each molecule type.
<li> 0: 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> 1: A template for this molecule type is read from towhee_template.
This template is then replicated throughout the simulation box to
generate an initial configuration.</li>
<li> 2: The coordinates for each atom are read from towhee_coords.
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>
</ul>
<dt><b>boxlx, boxly, boxlz (double precision)</b>
<ul>
<li> The initial box length (Angstroms) in the x,y, and z dimensions
for each box (one line per box).</li>
</ul>
<dt><b>initmol (integer)</b>
<ul>
<li> The initial number of each type of molecule in each box (one
line per box).</li>
</ul>
<dt><b>inix, iniy, iniz (integer)</b>
<ul>
<li> The initial number of molecules 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 (the sums of initmol).</li>
</ul>
<dt><b>inimix (integer)</b>
<ul>
<li> -1: molecules are initially placed in each box in alternating
order.</li>
<li> 0: molecules are initially placed in each box in random order.</li>
<li> 1: molecules are initially placed in each box order. Thus all
molecules of type 1 are placed in a box before any molecules of
type 2. If you are using initstyle = 2 then this is the only valid
option and the other options will be reset to this option by the
code.</li>
</ul>
<dt><b>rmtraa (double precision)</b>
<ul>
<li> The initial Atom-translation maximum displacement (Angstroms)
for all molecules types in all boxes. As the simulation progresses,
these values will be updated independently to give the desired acceptance
rate for each molecule type in each dimension of each box (see iratio).</li>
</ul>
<dt><b>rmtrac (double precision)</b>
<ul>
<li> The initial Center-of-mass translation maximum displacement (Angstroms)
for all molecule types in all boxes. As the simulation progresses,
these values will be updated independently to give the desired acceptance
rate for each molecule type in each dimension of each box (see iratio).</li>
</ul>
<dt><b>rmrot (double precision)</b>
<ul>
<li> The initial molecular rotation maximum displacement (radians)
for all molecule types in all boxes. As the simulation progresses,
these values will be updated independently to give the desired acceptance
rate for each molecule type about each axis of each box (see iratio).</li>
</ul>
<dt><b>rmvol (double precision)</b>
<ul>
<li> The initial volume maximum displacement. If this is an isobaric-isothermal
ensemble (lnpt = .true.) then this is the initial maximum volume
displacement (cubic Angstroms) in each box. If this is the canonical
Gibbs ensemble (lnpt = .false. 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><b>tatraa (double precision)</b>
<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 iratio) to yield this acceptance
rate. I typically use a value of 0.5, though some researchers prefer
smaller values.</li>
</ul>
<dt><b>tatrac (double precision)</b>
<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
iratio) to yield this acceptance rate. I typically use a value of
0.5, though some researchers prefer smaller values.</li>
</ul>
<dt><b>tarot (double precision)</b>
<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 iratio) to yield this acceptance rate. I typically
use a value of 0.5, though some researchers prefer smaller values.</li>
</ul>
<dt><b>tavol (double precision)</b>
<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><b>lnpt (logical)</b>
<ul>
<li> .true. if you want the volume moves to be performed in an exchange
with an external pressure bath (isobaric isothermal ensemble or
isobaric-isothermal Gibbs ensemble).</li>
<li> .false. if you do want the total volume of the system to be conserved.
In the case of a multi-box simulation this exchanges volume between
pairs of boxes (canonical Gibbs ensemble), in a single box case
no volume moves are allowed (canonical ensemble).</li>
</ul>
<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. If none of them are higher then you perform a rotation
move (in a sense pmrot is hardwired 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.</li>
<dt><b>pmvol (double precision)</b>
<ul>
<li> Probability of performing a volume move. If (lnpt = .true.) then
a single box is selected and it exchanges volume with an external
pressure bath (see pressure). If (lnpt = .false. and numboxes >
1) a pair of boxes are selected and volume is exchanged between
them.</li>
</ul>
<dt><b>pmvlpr (double precision)</b>
<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 (lnpt = .true.) then a value of pmvlpr is listed for each box.
If (lnpt = .false.) 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><b>pmswap, pmswmt (double precision)</b>
<ul>
<li> pmswap is the probability of performing an 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 coupled-decoupled
configurational-bias Monte Carlo. See the nch** variables down below
for more information about configurational-bias.</li>
<li> pmswmt is the probability of performing an interbox molecule
transfer move on each type of molecule in the system.</li>
</ul>
<dt><b>pmswpr (double precision)</b>
<ul>
<li> Probability of performing an 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><b>pmiswp, pmismt (double precision)</b>
<ul>
<li> pmiswp is the probability of performing an intrabox 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
coupled-decoupled configurational-bias Monte Carlo. See the nch**
variables down below for more information about configurational-bias.</li>
<li> pmismt is the probability of performing an intrabox molecule
transfer move on each type of molecule in the system.</li>
</ul>
<dt><b>pmcb, pmcbmt (double precision)</b>
<ul>
<li> pmcb is the 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. See the nch** variables down below
for more information about configurational-bias.</li>
<li> pmcbmt is the probability of performing a molecule regrowth on
each type of molecule in the system.</li>
</ul>
<dt><b>pmall (double precision)</b>
<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><b>pmback, pmbkmt (double precision)</b>
<ul>
<li> pmback is the probability of performing configurational-bias fixed-endpoint
regrowth of a portion of the protein backbone.
This move is still under development and is not yet fully functional. Please do
not use it until its status changes.</li>
<li> pmbkmt is the probability of performing a backbone regrowth
move on each type of molecule in the system.</li>
</ul>
<dt><b>pmtraat, pmtamt (double precision)</b>
<ul>
<li> pmtraa is the probability of performing a single-atom translation
move 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, chooses the
x,y, or z direction at random, and then attempts to displace the
atom a random distance between -rmtraa and +rmtraa in that direction.</li>
<li> pmtamt is the probability of performing a single-atom translation
move on each type of molecule in the system.</li>
</ul>
<dt><b>pmtracm, pmtcmt (double precision)</b>
<ul>
<li> pmtrac is the probability of performing a center-of-mass translation
move 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 the x,y, or z direction at random, and then attempts
to displace the entire molecule a random distance between -rmtrac
and +rmtrac in that direction.</li>
<li> pmtcmt is the probability of performing a center-of-mass translation
move on each type of molecule in the system.</li>
</ul>
<dt><b>pmromt (double precision)</b>
<ul>
<li> There is no specified value of pmrot as it is the move that is
performed if none of the other moves were selected. Thus it essentially
has a default value of 1.0. This move chooses a molecule of the
appropriate type at random, chooses the x,y, or z direction at random,
and then attempts to rotate the entire molecule about an x,y, or
z axis that runs through the center-of-mass a random number of radians
between -rmrot and +rmrot.</li>
<li> pmromt is the probability of performing a rotation move on each
type of molecule in the system.</li>
</ul>
<dt><b>cbstyle (integer)</b>
<ul>
<li> cbstyle = 0: When performing a configurational-bias move, generate trial bond lengths,
bending angles, and dihedral angles according to the true, ideal probability distribution.
This is the method described in M.G. Martin; J.I. Siepmann;
"Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for
phase equilibria. 2. united-atom description of branched alkanes",
<i>J. Phys. Chem. B</i> <b>103</b> 4508-4517 (1999).</li>
<li> cbstyle = 1: When performing a configurational-bias move, generate trial bond lengths,
bending angles, and dihedral angles according to a different probability density and then
fix this up in the acceptance rules. This work is still in progress and is not yet published.
</ul>
<dt><b>nchoi1 (integer)</b>
<ul>
<li> This is the number of trial positions that are sampled for the
first atom inserted during a configurational-bias molecule exchange
move (see pmswp and pmiswp). I typically use a value of 10. The
value must be less than or equal to NCHMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nchoi (integer)</b>
<ul>
<li> This is the number of trial positions that are sampled for all
atoms except for the first atom inserted during a configurational-bias
molecule exchange move (see pmswp and pmiswp). This is used for
all atoms in a configurational-bias regrowth move (see pmcb). I
typically use a value of 10. The value must be less than or equal
to NCHMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nchtor (integer)</b>
<ul>
<li> This is the number of trial dihedral angles that are sampled
during configurational-bias moves. I typically use a value in the
range 100 to 360. The value must be less than or equal to NCHTOR_MAX
(see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nchconn (integer)</b>
<ul>
<li> This is the number of trial dihedral angles that are sampled
during configurational-bias 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 also could
be used to regrow the interiors of large molecules (not yet implemented).
I typically use a value in the range 200 to 360. The value must
be less than or equal to NCHTOR_MAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nchbna (integer)</b>
<ul>
<li> This is the number of trial angles that are sampled during configurational-bias
moves when we are selecting the iugrow-iufrom-iuprev angle (see
the section on configurational-bias). I typically use a value of
1000.</li>
</ul>
<dt><b>nchbnb (integer)</b>
<ul>
<li> This is the number of trial angles that are sampled during configurational-bias
moves when we are selecting the rotation about a cone of one of
the iugrow angles relative to the others (see the section on configurational-bias).
I typically use a value of 1000.</li>
</ul>
<dt><b>nchvib (integer)</b>
<ul>
<li> This is the number of trial bond lengths that are sampled during
configurational-bias moves when we are growing atoms. I typically
use a value of 1000 unless I am using a fixed-bond length force
field, in which case you might as well use 1.</li>
</ul>
<dt><b>vibrang (double precision, double precision)</b>
<ul>
<li> This is the range of bond lengths to sample via configurational-bias
Monte Carlo. The range is expressed as a fraction of the equilibrium
bond length for the lower bound and the upper bound. I usually values
of 0.85 and 1.15. These values are only used for cbstyle=0, but you must still
specifiy values even if you are using a different cbstyle</li>
</ul>
<dt><b>sdevtor (double precision)</b>
<ul>
<li> This is the standard deviation of a gaussian distribution that is used to
sample dihedral angles [on 0,360] during a configurational-bias regrowth if cbstyle=1. Specify
a value in degrees. Right now I am using a value of 20.0. If cbstyle is not 1 then
this value is not used in the code, but must still be entered into the input file.
</ul>
<dt><b>sdevbena (double precision)</b>
<ul>
<li> This is the standard deviation of a gaussian distribution that is used to
generate trials for the part A bending angles [on 0,180] during a configurational-bias regrowth if cbstyle=1. Specify
a value in degrees. Right now I am using a value of 10.0. If cbstyle is not 1 then
this value is not used in the code, but must still be entered into the input file.
</ul>
<dt><b>sdevbenb (double precision)</b>
<ul>
<li> This is the standard deviation of a gaussian distribution that is used to
generate trials for the part B bending angles [on 0,360] during a configurational-bias regrowth if cbstyle=1. Specify
a value in degrees. Right now I am using a value of 20.0. If cbstyle is not 1 then
this value is not used in the code, but must still be entered into the input file.
</ul>
<dt><b>sdevvib (double precision)</b>
<ul>
<li> This is the standard deviation of a gaussian distribution that is used to
sample bond lengths during a configurational-bias regrowth if cbstyle=1. Specify
a value in Angtroms. Right now I am using a value of 0.1. If cbstyle is not 1 then
this value is not used in the code, but must still be entered into the input file.
</ul>
<li> The final section of towhee_input contains the information that
is used to construct the forcefield for the molecule types in the
system. There are three different ways to set up this section that
depend on inpstyle. The first way requires an explicit declaration
of the entire force field and while it allows the most flexibility,
is quite a burden to set up for any molecule with more than 10 atoms.
The second option is an automated builder which works for any molecule,
so long as the force field you wish to use has been implemented properly
into the code. The final option is a builder for proteins, or other
amino acid sequences. The choice of inpstyle determines what happens
below it so all of the remaining variables are described in each case
of inpstyle.</li>
<dt><b>inpstyle (integer)</b>
<ul>
<li> 0: Explicit declaration of all terms of the force field that describes
this molecule type. This is the hardest way to set up the molecule
information, but it also allows for the most flexibility. I do not
recommend using this option unless it is not possible to use the more
sophisticated options for the molecule of interest.</li>
<dt>
<b>nunit (integer) </b>
<ul>
<li> The number of atoms (or united-atoms) in this molecule. Must
be less than or equal to NUMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>nmaxcbmc (integer)</b>
<ul>
<li> The maximum number of atoms to regrow during a configurational-bias
regrowth. Generally I set this to the same value as nunit, but
occasionally a molecule is so large that almost none of the moves
which regrow large portions are accepted. In this case I set nmaxcbmc
to be around 1/2 of nunit so that only smaller regrowths are performed.</li>
</ul>
<dt><b>lelect (logical) </b>
<ul>
<li> .true. if you want coulombic interactions computed for this
molecule.</li>
<li> .false. if you only want the van der Waals terms. The code
runs a bit faster if lelect is false so it is worth setting if
you are not using coulombic terms.</li>
</ul>
<dt><b>lpdb (logical) </b>
<ul>
<li> .true. if you want to input information about the pdb (protein
data bank) atom name, amino acid number, amino acid name. This
information is needed in order to use the cartoon feature of certain
pdb viewers (such as Rasmol).</li>
<li> .false. if you don't need that feature. A pdb file will still
be output using the atom types defined in ffnonbond so you can
still view the system, you just can not use the cartoon feature.</li>
</ul>
<p><font color="red"> The variables listed immediately below (unit
through improper stereo) are listed as a group for each atom in
the molecule. Thus, you input all of the information about the first
atom before you list information for the subsequent atoms.</font>
<dt><b>unit (integer), ntype (integer), qqatom (double precision) </b>
<ul>
<li> unit is the number of the atom in order starting from atom
number 1. This is only used to help the user keep track of the
molecule as they are building it in the input file. If the unit
number listed in towhee_input does not match the running total
of unit numbers in Towhee then the code will stop with an error
message.</li>
<li> ntype is the integer that ffnonbond uses to determine the force
field parameters. You will need to look in ffnonbond.F in order
to find the number that you wish to use.</li>
<li> qqatom is the charge on this atom. This value is not used (but
must still be input) if lelect is false.</li>
</ul><dt>
<b>pdbname (character), aminonum (integer), aminoshort (character) </b>
<ul><dt>
These variables only need to be listed if lpdb = .true.
<li> pdbname: A four letter/number string that is output in the pdb
file. The precise spacing is important if you want to get most pdb
viewers to recognize the atoms as the pdb file is extremely specific.</li>
<li> aminonum: The number of each amino acid starting from the N-terminus.</li>
<li> aminoshort: The three letter code for each amino acid, or other
group (such as caps on the C or N termini).</li>
</ul><dt>
<b>vibration</b>
<ul><dt>
<b>invib (integer) </b>
<ul>
<li> The first line under the vibration heading is the number of
atoms that are bonded to the current atom. Must be a number between
0 and NNBOND (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>ijvib (integer), itvib (integer) </b>
<ul>
<li> The next <b>invib</b> lines underneath the vibration heading
are a list of the bond partner and bond force field number (see
ffbond.F) for the <b>invib</b> atoms that are bonded to the
current atom. Thus if you have 4 vibrations the next 4 lines
will list the bond partner and bond force field number for each
bond.</li>
</ul>
</ul><dt>
<b>bending</b>
<ul><dt>
<b>inben (integer) </b>
<ul>
<li> The first line under the bending heading is the number of bond
bending angles that terminate at the current atom. You must list
all bond bending angles which have the current atom at one of
the ends, but you do not list bond bending angles which contain
the current atom in the center. Must be a number between 0 and
NNBOND*(NNBOND-1) (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>ijben2 (integer), ijben3(integer), itben (integer) </b>
<ul>
<li> The next <b>inben</b> lines underneath the bending heading
are a list of the other atoms in the bond bending angle and
the bond bending angle force field number (see ffangle.F) for
the <b>inben</b> angles that contain the current atom at one
of the ends. The format for listing the angle is to consider
the current atom in the first position of an angle between atoms
current-ijben2-ijben3 so you only need to list atoms ijben2
and ijben3 and the bending type on each line, where there is
one angle per line of towhee_input.</li>
</ul>
</ul><dt>
<b>torsion</b>
<ul><dt>
<b>intor (integer) </b>
<ul>
<li> The first line under the torsion heading is the number of dihedral
angles (regular torsions) that terminate at the current atom.
You must list all regular torsion angles which have the current
atom at one of the ends, but you do not list regular torsion angles
which contain the current atom in the center. Must be a number
between 0 and NNBOND*(NNBOND-1)*(NNBOND-1) (see <a href="../code/code_manual.html#preproc">preproc.h</a>).</li>
</ul>
<dt><b>ijtor2 (integer), ijtor3(integer), ijtor4 (integer), ittor
(integer) </b>
<ul>
<li> The next <b>intor</b> lines underneath the torsion heading
are a list of the other atoms in the regular torsion angle and
the torsion force field number (see fftorsion.F) for the <b>intor</b>
torsions that contain the current atom at one of the ends. The
format for listing the regular torsion angle is to consider
the current atom in the first position of a dihedral between
atoms current-ijtor2-ijtor3-ijtor4 so you only need to list
atoms ijtor2, ijtor3, and ijtor4 and the torsion type on each
line, where there is one regular torsion per line of towhee_input.</li>
</ul>
</ul><dt>
<b>angle-angle</b>
<ul><dt>
<b>inaa (integer) </b>
<ul>
<li> The first line under the angle-angle heading is the number
of angle-angle terms which have their shared central atom located
at the current atom. You must list all angle-angle terms which
have the current atom at the shared central position, but you
do not list angle-angle terms which contain the current atom at
one of the ends. Must be a number between 0 and (NNBOND*(NNBOND-1))/2
(see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijaa0 (integer), ijaa1(integer), ijaa2 (integer), itaa (integer)
</b>
<ul>
<li> The next <b>inaa</b> lines underneath the angle-angle heading
are a list of the other atoms in the angle-angle term and and
the angle-angle force field number (see ffangang.F) for the
<b>inaa</b> angle-angle terms that contain the current atom
at the shared central atom. The format for listing the regular
torsion angle is to consider the current atom as the central
shared atom in the angle-angle term between the angles ijaa0-current-ijaa1
and ijaa0-current-ijaa2. Each angle-angle term is listed on
one line according to the format ijaa0, ijaa1, ijaa2 and itaa
(the angle-angle type). </li>
</ul>
</ul><dt>
<b>improper oop</b>
<ul><dt>
<b>inimpc (integer) </b>
<ul>
<li> The first line under the improper oop heading is the number
of improper torsions (out-of-plane) which have the central atom
located at the current atom. You must list all improper torsions
(out-of-plane) which have the current atom at the central position,
but you do not list improper torsions (out-of-plane) which contain
the current atom at one of the ends. Must be a number between
0 and ((NNBOND-1)*(NNBOND-2))/2 (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijimpc2 (integer), ijimpc3(integer), ijimpc4 (integer), itimpc
(integer) </b>
<ul>
<li> The next <b>inimpc</b> lines underneath the improper torsion
(out-of-plane) heading are a list of the other atoms in the
improper torsion (oop) and the torsion force field number (see
fftorsion.F) for the <b>inimpc</b> improper torsions (oop) that
contain the current atom at the central atom. This type of improper
torsion works the same way as a regular torsion, except that
the first atom is generally bonded to the three other atoms.
The format for listing the improper torsion (oop) is to consider
the current atom in the first position of a dihedral between
atoms current-ijimpc2-ijimpc3-ijimpc4 so you only need to list
atoms ijimpc2, ijimpc3, and ijimpc4 and the torsion type on
each line, where there is one improper torsion (oop) per line
of towhee_input. </li>
</ul>
</ul><dt>
<b>improper stereo</b>
<ul><dt>
<b>inimpc (integer) </b>
<ul>
<li> The first line under the improper stereo heading is the number
of improper torsions (stereogenic) which have the central atom
located at the current atom. You must list all improper torsions
(stereo) which have the current atom at the central position,
but you do not list improper torsions (stereo) which contain the
current atom at one of the ends. Must be a number between 0 and
((NNBOND-1)*(NNBOND-2))/2 (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijimpa2 (integer), ijimpa3(integer), ijimpa4 (integer), itimpa
(integer) </b>
<ul>
<li> The next <b>inimpa</b> lines underneath the improper torsion
(stereo) heading are a list of the other atoms in the improper
torsion (stereo) and the torsion force field number (see fftorsion.F)
for the <b>inimpa</b> improper torsions (stereo) that contain
the current atom at the central atom. This type of improper
torsion works by computing the dihedral angle between the planes
formed by the atoms ijimpa2-current-ijimpa3 and ijimpa2-current-ijimpa4.
This was originally used as a means to enforce planarity, but
is also useful for enforcing stereochemistry. The format for
the improper torsion (stereo) is to list atoms ijimpa2, ijimpa3,
and ijimpa4 and the torsion type (itimpa) on each line, where
there is one improper torsion (stereo) per line of towhee_input. </li>
</ul>
</ul>
<dt><font color="red"> This is the end of the section that is repeated
for each atom for inpstyle=0 </font>
<p> </p>
<li> 1: Polypeptide builder which sets up everything using buildprot
and assemble routines. This sets up everything for proteins from
a list of the amino acids. This routine also could be used to build
polymers, but I have not yet coded in any non-peptide monomers.
I am working on some documentation of the currently available monomers,
but until that is complete you will have to look into buildprot.F
to see what is available. </li>
<dt><b>nunit (integer) </b>
<ul>
<li> The number of monomers in this molecule. Must be less than
or equal to NUMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>) and there is also a check in
the builder to make sure you do not exceed NUMAX with the number
of atoms that all of your monomers require. </li>
</ul>
<dt><b>nmaxcbmc (integer)</b>
<ul>
<li> The nmaxcbmc variable determines the largest number of atoms
that are regrown during a configurational-bias regrowth. Since
we only know the number of amino acids at this stage, and not
the number of atoms, the final value of nmaxcbmc is computed as
the product of the final number of atoms in the molecule times
the input value of nmaxcbmc divided by the input value of nunit. </li>
</ul>
<dt><b>lelect (logical) </b>
<ul>
<li> .true. if you want coulombic interactions computed for this
molecule.</li>
<li> .false. if you only want the van der Waals terms. The code
runs a bit faster if lelect is false so it is worth setting if
you are not using coulombic terms. </li>
</ul>
<dt><b>forcefield (character) </b>
<ul>
<li> The forcefield that you want to use to build this molecule.
I'm working on better documentation of which force fields are
implemented, but until that is finished just take a look in ffnonbond.F </li>
</ul>
<dt><b>protgeom (character) </b>
<ul>
<li> linear: The polypeptide will be generated starting from the
N-terminus and finishing at the C-terminus. </li>
<li> cyclic: The polypeptide is cyclic so the first amino acid is
bonded to the final amino acid. </li>
</ul>
<p><font color="red"> The variables listed immediately below are listed
as a group for each amino acid in the molecule. There is only one
line of input per building block in the molecule.</font>
<dt><b>pepname (character), stereochem (character), bondpartner (integer)
</b>
<ul>
<li> pepname is a two letter code for the building blocks of the
molecule. Peptides use a code where the first letter is the one
letter code for each amino acid. The second character is generally
the charge state of the side chain, but has some different meanings
for histidine and cysteine. Until the documentation is in place
you need to look in buildprot.F to find a complete list of valid
pepnames. </li>
<li> stereochem is a single letter which determines the stereochemistry
of the peptide. The valid options are l (L-amino acid), d (D-amino
acid) and r (racemic). </li>
<li> bondpartner is the number of the amino acid which is bonded
to this amino acid through the side chain. This is only used for
cysteines which have a disulfide bridge (type cs), otherwise just
set this value to 0. The bondpartner integers refer to the amino
acids starting with the first amino acid listed in towhee_input
as amino acid #1. </li>
</ul>
<dt><font color="red"> This is the end of the section that is repeated
for each atom for inpstyle=1 </font>
<p> </p>
<li> 2: Atom-based connectivity map, with the details of the force
field parameters determined via the buildmolec and assemble routines.
This is the easiest way to set up any molecule that is not a series
of amino acids. You must choose a forcefield and then input the
appropriate parameter names for that force field. I'm working on
better documentation of the atom names used in Towhee, but until
that is complete you have to look in ffnonbond.F The program will
sort out all of the vibration types, bending angles, bending types,
regular torsion angles, regular torsion types, angle-angle terms,
angle-angle types, improper torsion (oop) types, and improper torsion
(stereo) types that are implied by the bonding structure of the
molecule. I have not automated the atom assignment for the improper
torsions as some of the force fields do not have general rules (at
least not rules I can decipher) for determining where the improper
torsions belong. </li>
<dt><b>nunit (integer) </b>
<ul>
<li> The number of atoms (or united-atoms) in this molecule. Must
be less than or equal to NUMAX (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>nmaxcbmc (integer)</b>
<ul>
<li> The maximum number of atoms to regrow during a configurational-bias
regrowth. Generally I set this to the same value as nunit, but
occasionally a molecule is so large that almost none of the moves
which regrow large portions are accepted. In this case I set nmaxcbmc
to be around 1/2 of nunit so that only smaller regrowths are performed. </li>
</ul>
<dt><b>lelect (logical) </b>
<ul>
<li> .true. if you want coulombic interactions computed for this
molecule.</li>
<li> .false. if you only want the van der Waals terms. The code
runs a bit faster if lelect is false so it is worth setting if
you are not using coulombic terms. </li>
</ul>
<dt><b>forcefield (character) </b>
<ul>
<li> The forcefield that you want to use to build this molecule.
I'm working on better documentation of which force fields are
implemented, but until that is finished just take a look in ffnonbond.F </li>
</ul>
<p><font color="red"> The variables listed immediately below (unit
through improper stereo) are listed as a group for each atom in
the molecule. Thus, you input all of the information about the first
atom before you list information for the subsequent atoms.</font>
<dt><b>unit (integer), type (character), qqatom (double precision) </b>
<ul>
<li> unit is the number of the atom in order starting from atom
number 1. This is only used to help the user keep track of the
molecule as they are building it in the input file. If the unit
number listed in towhee_input does not match the running total
of unit numbers in Towhee then the code will stop with an error
message. </li>
<li> ntype is the character string that contains the atom type for
the forcefield. I'm working on better documentation for the available
atom types, but until that is ready you will need to look in ffnonbond.F.
I generally use the same atom types as the original authors of
the force field, but sometimes I have to add information to those
atom types in order to automate the assembly process. </li>
<li> qqatom is the charge on this atom. This value is not used (but
must still be input) if lelect is false. </li>
</ul><dt>
<b>vibration</b>
<ul><dt>
<b>invib (integer) </b>
<ul>
<li> The first line under the vibration heading is the number of
atoms that are bonded to the current atom. Must be a number between
0 and NNBOND (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijvib (integer)</b>
<ul>
<li> The second line contains the atom numbers for all <b>invib</b>
atoms that are bonded to the current atom. </li>
</ul>
</ul><dt>
<b>improper oop</b>
<ul><dt>
<b>inimpc (integer) </b>
<ul>
<li> The first line under the improper oop heading is the number
of improper torsions (out-of-plane) which have the central atom
located at the current atom. You must list all improper torsions
(out-of-plane) which have the current atom at the central position,
but you do not list improper torsions (out-of-plane) which contain
the current atom at one of the ends. Must be a number between
0 and ((NNBOND-1)*(NNBOND-2))/2 (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijimpc2 (integer), ijimpc3(integer), ijimpc4 (integer), itimpc
(integer) </b>
<ul>
<li> The next <b>inimpc</b> lines underneath the improper torsion
(out-of-plane) heading are a list of the other atoms in the
improper torsion (oop) and the torsion force field number (see
fftorsion.F) for the <b>inimpc</b> improper torsions (oop) that
contain the current atom at the central atom. This type of improper
torsion works the same way as a regular torsion, except that
the first atom is generally bonded to the three other atoms.
The format for listing the improper torsion (oop) is to consider
the current atom in the first position of a dihedral between
atoms current-ijimpc2-ijimpc3-ijimpc4 so you only need to list
atoms ijimpc2, ijimpc3, and ijimpc4 and the torsion type on
each line, where there is one improper torsion (oop) per line
of towhee_input. If you want the program to determine the improper
torsion (oop) type then just enter an itimpc value of 0. </li>
</ul>
</ul><dt>
<b>improper stereo</b>
<ul><dt>
<b>inimpc (integer) </b>
<ul>
<li> The first line under the improper stereo heading is the number
of improper torsions (stereogenic) which have the central atom
located at the current atom. You must list all improper torsions
(stereo) which have the current atom at the central position,
but you do not list improper torsions (stereo) which contain the
current atom at one of the ends. Must be a number between 0 and
((NNBOND-1)*(NNBOND-2))/2 (see <a href="../code/code_manual.html#preproc">preproc.h</a>). </li>
</ul>
<dt><b>ijimpa2 (integer), ijimpa3(integer), ijimpa4 (integer), itimpa
(integer) </b>
<ul>
<li> The next <b>inimpa</b> lines underneath the improper torsion
(stereo) heading are a list of the other atoms in the improper
torsion (stereo) and the torsion force field number (see fftorsion.F)
for the <b>inimpa</b> improper torsions (stereo) that contain
the current atom at the central atom. This type of improper
torsion works by computing the dihedral angle between the planes
formed by the atoms ijimpa2-current-ijimpa3 and ijimpa2-current-ijimpa4.
This was originally used as a means to enforce planarity, but
is also useful for enforcing stereochemistry. The format for
the improper torsion (stereo) is to list atoms ijimpa2, ijimpa3,
and ijimpa4 and the torsion type (itimpa) on each line, where
there is one improper torsion (stereo) per line of towhee_input.
If you want the program to figure out the improper torsion (stereo)
type then just input an itimpa value of 0. </li>
</ul>
</ul>
<dt><font color="red"> This is the end of the section that is repeated
for each atom for inpstyle=2 </font>
</ul>
</ul>
<a href="../index.html">Return to the main towhee web page</a>
<p> </p>
</td>
</tr>
</table>
<hr width="715" align="left">
<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>
<i>Last updated:</i>
<!-- #BeginDate format:Am1 -->September 14, 2004<!-- #EndDate -->
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