MCCCS Towhee - Version 7.0.4 (September 18 2012)
Copyright (C) <2012> Marcus G. Martin
Code Contributors for 2012: Marcus G. Martin;
Copyright (C) <2011> Marcus G. Martin
Code Contributors for 2011: Fred James; Marcus G. Martin; Suleiman Oloriegbe;
Copyright (C) <2010> Marcus G. Martin
Code Contributors for 2010: Rene Haber; Andrej Lajovic; Marcus G. Martin; Loukas Peristeras;
Copyright (C) <2009> Marcus G. Martin
Code Contributors for 2009: Rene Haber; Marcus G. Martin; Loukas Peristeras;
Copyright (C) <2008> Marcus G. Martin
Code Contributors for 2008: Rene Haber; Iyad A. Hijazi; Marcus G. Martin; Loukas Peristeras; Craig Tenney;
Copyright (C) <2007> Marcus G. Martin
Code Contributors for 2007: Bernhard Eckl; Frank Heilmann; Jianhui Li; Marcus G. Martin; Craig M. Tenney; Ozgur Yazaydin
Copyright (C) <2006> Marcus G. Martin
Code Contributors for 2006: Alan A. Chen; Arben Jusufi; Christian D. Lorenz; Marcus G. Martin; Jeffrey J. Potoff; Vincent K. Shen; Matthew A. Wyczalkowski; Ozgur Yazaydin
Copyright (C) <2005> Marcus G. Martin
Code Contributors for 2005: Marcus G. Martin; Alan A. Chen; Christian D. Lorenz; Matthew A. Wyczalkowski
Copyright (C) <2004> Marcus G. Martin
Code Contributors for 2004: Marcus G. Martin; Christian D. Lorenz; Peter A. Schultz; Aidan P. Thompson; Jeffrey J. Potoff; Steve R. Lustig; Paul S. Crozier; Nicholas du Preez
Copyright (C) <2003> Marcus G. Martin
Code Contributors for 2003: Marcus G. Martin; Christian D. Lorenz; David B. Ritch; Michael L. Greenfield; Yogesh Srivastava; Evangelos A Coutsias
Copyright (C) <2002> Marcus G. Martin
Code Contributors for 2002: Marcus G. Martin; Christian D. Lorenz; Aidan P. Thompson; Allen G. Sault
Copyright (C) <2000-2001> Marcus G. Martin
Copyright (C) <1999> J. Ilja Siepmann and Marcus G. Martin
Code Contributors for 1999: J. Ilja Siepmann; Marcus G. Martin; Bin Chen; Collin D. Wick; John Stubbs
Direct comments about this code to Marcus G. Martin (marcus_martin@users.sourceforge.net)
See the MCCCS Towhee web site for more information and the users manual.
http://towhee.sourceforge.net
We would like to thank the following agencies for providing funding used to develop MCCCS Towhee
-Department of Energy Industrial Technologies Program (MGM)
-National Science Foundation (JIS)
-Department of Energy Computational Science Graduate Fellowship (MGM,CDW)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Reading from towhee_input file: towhee_input
in directory: current directory
inputformat: Towhee
ensemble: npt
temperature: 1.00000
pressure: 1.00000
nmolty: 2
nmolectyp: 13 76
numboxes: 1
stepstyle: cycles
nstep: 1
printfreq: 100
blocksize: 100
moviefreq: 100
backupfreq: 100
runoutput: full
Full output of updates and block averages
pdb_output_freq: 10
loutlammps: T
pressurefreq: 1000
trmaxdispfreq: 1
volmaxdispfreq: 1
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_ParkHijazi
classical_potential: Embedded Atom Method
READCLASSICAL: pot_num: 111 potential name: Embedded Atom Method
interpolatestyle: cubicspline
Tables interpolated using cubic splines
rcut: 1.00000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Explicit declaration of Cross Terms
Please check the forcefield file carefully
default max_bond_length: 3.00
ntypes 2
numone,lhere 1 F
numone,lhere 2 F
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
coords coords
Box: 1 initlattice: none none
Box: 1 initmol: 13 76
Box: 1 inix,iniy,iniz: 5 5 5
Box idim hmatrix: 1 1 14.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 14.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 14.00000
pm1boxcbswap: 0.00000
pm1cbswmt: 0.500000 1.00000
pm1boxcomswitch: 1.00000
pm1comswbox: 1.00000
pm1comswpair: 1.00000
pmplane: 0.00000
pmplanebox: 1.00000
planewidth: 1.00000
pmrow: 0.00000
pmrowbox: 1.00000
rowwidth: 1.00000
pmtracm: 0.00000
pmtcmt: 0.500000 1.00000
rmtrac: 0.500000
tatrac: 0.500000
cbmc_formulation: Martin and Frischknecht 2006
Coupled to pre-nonbond formulation from
M.G. Martin; A.L. Frischknecht; Mol. Phys. 104 2439-2456 (2006)
cbmc_setting_style: Martin and Frischknecht
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the ParkHijazi force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:Cu charge: 0.00000
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the ParkHijazi force field
charge_assignment: manual
Building the input file for molecule type: 2
unit: 1 name:Au charge: 0.00000
Verifying input structures are consistent
Determining CBMC bond distributions
Determining Autofit Gaussian bend A parameters
Determining Autofit Gaussian bend B parameters
Determining Autofit Gaussian dihedral parameters
Determining cyclic subunits for molecule type 1
Determining cyclic subunits for molecule type 2
Default total charge on molecule 1 is 0.00000
Default total charge on molecule 2 is 0.00000
Total charge in the simulation system: 0.00000
Bond Types
No Bond Types
Angle Types
No Angle Types
Torsion Types
No Torsion Types
Improper Torsion Types
No Improper Types
SETCLASSICAL: adjusted rcut to be the maximum distance from tabulated potential
New rcut value is 6.68250
Isobaric-isothermal ensemble
3-dimensional periodic box
Additional Center-of-Mass cutoff
Coupled-decoupled Configurational-bias MC
Molecular mass for molecule type 1 is 63.5500 g/mol
Molecular mass for molecule type 2 is 196.9700 g/mol
Calling initconf
Selected random number generator DX-1597-2-7 and single integer seed 1302002
Testing random number generator using the single integer seed
0.812479 0.687663 0.080298 0.200888 0.516914
10 million RNG sum (approximately 5 million): 4999978.2264809748
Box idim hinverse: 1 1 0.07143 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.07143 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.07143
Finished initconf
Energies exclusively from internal potentials
Nonbonded Force Field
Embedded-Atom potential
U = eam_pair(r) + eam_embed[ Sum[eam_dens(r)] ]
Number of MC cycles: 1
Number of molecules: 89
Temperature [K]: 1.00000
External pressure [kPa]: 1.00000
Initial Energies for Box 1
Total molecules in this box 89
Molecules of type 1 : 13
Molecules of type 2 : 76
total vibration 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -1755365.291 [K] -3488.28972 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 396837.070 [K] 788.60091 [kcal/mol]
3-body nonbond -2152202.361 [K] -4276.89063 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1755365.2913 [K] -3488.289717 [kcal/mol]
Total energy [eV] -151.267
initial virial pressure in box 1 = 447.81
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
Updating maximum translational/rotational displacements
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 14.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 14.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 14.00000
* SWITCH Moves *
Molecule pair: 1 Box: 1 Attempts: 89. Accepted: 2. Accepted: 2.247 %
Final Energies for Box 1
Total molecules in this box 89
Molecules of type 1 : 13
Molecules of type 2 : 76
total vibration 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -1803940.394 [K] -3584.81893 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 376431.453 [K] 748.05055 [kcal/mol]
3-body nonbond -2180371.847 [K] -4332.86948 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1803940.3938 [K] -3584.818930 [kcal/mol]
Total energy [eV] -155.452
Averages Units Type Box 1
Volume nm^3 0.27440E+01
Volume^2 nm^6 0.75295E+01
Molecule Number 1 13.000
Molecule Number 2 76.000
Molar Volume ml/mol 0.18567E+02
Specific Density g/ml 9.55906572
Number Density nm-3 1 4.73761
Number Density nm-3 2 27.69679
Mole Fraction 1 0.1460674
Mole Fraction 2 0.8539326
Radius of Gyration A 1 0.0000000
Radius of Gyration A 2 0.0000000
Ideal Pressure kPa 0.44794E+03
Ideal p_i <N/V>kT kPa 1 0.65429E+02
Ideal p_i <N/V>kT kPa 2 0.38251E+03
Total Classical K -0.1803E+07
Inter vdw K -0.1803E+07
Angle K 0.0000E+00
Torsion K 0.0000E+00
Intra vdw K 0.0000E+00
External Field K 0.0000E+00
Vibration K 0.0000E+00
Coulomb K 0.0000E+00
Tail vdw K 0.0000E+00
Solvation K 0.0000E+00
G: Sum{<u_i><N_i>} kJ/mol 0.0000E+00
U kJ/mol -0.1499E+05
Please see towhee_citations for a list of suggested citations for this simulation
