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: nvt
temperature: 336.000
nmolty: 4
nmolectyp: 1 1 1 1
numboxes: 1
stepstyle: cycles
nstep: 1
printfreq: 1
blocksize: 2000
moviefreq: 100000
backupfreq: 1000
runoutput: full
Full output of updates and block averages
pdb_output_freq: 100000
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_Shukla1987
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Shukla
lshift: F
ltailc: T
rmin: 1.00000
rcut: 10.0000
rcutin: 10.0000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Mixing rules from Equations 19 and 20 of
K.P. Shukla Mol. Phys. 62, 5, 1143-1163 (1987)
with cross terms adjusted by polarizabilities
default max_bond_length: 3.00
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
full cbmc full cbmc full cbmc full cbmc
Box: 1 initlattice: simple cubic simple cubic simple cubic simple cubic
Box: 1 initmol: 1 1 1 1
Box: 1 inix,iniy,iniz: 8 8 7
Box idim hmatrix: 1 1 30.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 30.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 30.00000
pmtracm: 1.00000
pmtcmt: 0.250000 0.500000 0.750000 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 Shukla1987 force field
charge_assignment: none
Building the input file for molecule type: 1
unit: 1 name:Xe
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the Shukla1987 force field
charge_assignment: none
Building the input file for molecule type: 2
unit: 1 name:CH4
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the Shukla1987 force field
charge_assignment: none
Building the input file for molecule type: 3
unit: 1 name:Ar
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the Shukla1987 force field
charge_assignment: none
Building the input file for molecule type: 4
unit: 1 name:Kr
Verifying input structures are consistent
Determining CBMC bond distributions
for molecule type 1
for molecule type 2
for molecule type 3
for molecule type 4
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
Determining cyclic subunits for molecule type 3
Determining cyclic subunits for molecule type 4
Default total charge on molecule 1 is 0.00000
Default total charge on molecule 2 is 0.00000
Default total charge on molecule 3 is 0.00000
Default total charge on molecule 4 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
Canonical ensemble
3-dimensional periodic box
Additional Center-of-Mass cutoff
Dual Cutoff Configurational-bias Monte Carlo
Coupled-decoupled Configurational-bias MC
Molecular mass for molecule type 1 is 131.2900 g/mol
Molecular mass for molecule type 2 is 16.0426 g/mol
Molecular mass for molecule type 3 is 39.9480 g/mol
Molecular mass for molecule type 4 is 83.8000 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 0.03333 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.03333 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.03333
INITCONF: building template for molecule type: 1
Initial Structure Growth Trial: 1
INITCONF: building template for molecule type: 2
Initial Structure Growth Trial: 1
INITCONF: building template for molecule type: 3
Initial Structure Growth Trial: 1
INITCONF: building template for molecule type: 4
Initial Structure Growth Trial: 1
Finished initconf
Energies exclusively from internal potentials
Nonbonded Force Field
Lennard-Jones 12-6 potential
with tail corrections
u(r) = 4*epsilon[(sigma/r)^12 - (sigma/r)^6] - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4sig 1-4eps
1 Ar 1 Ar 3.4040 117.7000 0.0000 0.0000 0.0000
1 Ar 2 Kr 3.5190 136.9202 0.0000 0.0000 0.0000
1 Ar 3 Xe 3.7054 152.4793 0.0000 0.0000 0.0000
1 Ar 4 CH4 3.5763 130.0354 0.0000 0.0000 0.0000
2 Kr 2 Kr 3.6220 164.1100 0.0000 0.0000 0.0000
2 Kr 3 Xe 3.7938 189.3185 0.0000 0.0000 0.0000
2 Kr 4 CH4 3.6775 156.7432 0.0000 0.0000 0.0000
3 Xe 3 Xe 3.9480 227.8600 0.0000 0.0000 0.0000
3 Xe 4 CH4 3.8474 182.1178 0.0000 0.0000 0.0000
4 CH4 4 CH4 3.7330 149.9200 0.0000 0.0000 0.0000
Number of MC cycles: 1
Number of molecules: 4
Temperature [K]: 336.00000
Initial Energies for Box 1
Total molecules in this box 4
Molecules of type 1 : 1
Molecules of type 2 : 1
Molecules of type 3 : 1
Molecules of type 4 : 1
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 -93.698 [K] -0.18620 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -91.602 [K] -0.18203 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -2.096 [K] -0.00417 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -93.69824990 [K] -0.1861986467 [kcal/mol]
initial virial pressure in box 1 = 2167.27
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 -0.1954E+03 0.2700E+05 2167.3 1 1 1 1
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 30.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 30.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 30.00000
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 1. Accepted: 1. Accepted: 100.000 %
Molecule: 2 Box: 1 Attempts: 2. Accepted: 0. Accepted: 0.000 %
Molecule: 4 Box: 1 Attempts: 1. Accepted: 1. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 4
Molecules of type 1 : 1
Molecules of type 2 : 1
Molecules of type 3 : 1
Molecules of type 4 : 1
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 -195.363 [K] -0.38823 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -193.267 [K] -0.38406 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -2.096 [K] -0.00417 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -195.36292758 [K] -0.3882283048 [kcal/mol]
Averages Units Type Box 1
Volume nm^3 0.27000E+02
Volume^2 nm^6 0.72900E+03
Molecule Number 1 1.000
Molecule Number 2 1.000
Molecule Number 3 1.000
Molecule Number 4 1.000
Molar Volume ml/mol 0.40649E+04
Specific Density g/ml 0.01667211
Number Density nm-3 1 0.03704
Number Density nm-3 2 0.03704
Number Density nm-3 3 0.03704
Number Density nm-3 4 0.03704
Mole Fraction 1 0.2500000
Mole Fraction 2 0.2500000
Mole Fraction 3 0.2500000
Mole Fraction 4 0.2500000
Radius of Gyration A 1 0.0000000
Radius of Gyration A 2 0.0000000
Radius of Gyration A 3 0.0000000
Radius of Gyration A 4 0.0000000
Ideal Pressure kPa 0.68746E+03
Ideal p_i <N/V>kT kPa 1 0.17187E+03
Ideal p_i <N/V>kT kPa 2 0.17187E+03
Ideal p_i <N/V>kT kPa 3 0.17187E+03
Ideal p_i <N/V>kT kPa 4 0.17187E+03
Total Classical K -0.8864E+02
Inter vdw K -0.8864E+02
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 -0.2096E+01
Solvation K 0.0000E+00
G: Sum{<u_i><N_i>} kJ/mol 0.0000E+00
U kJ/mol -0.7370E+00
C_v: T^2<H^2>-<H>^2 J/K mol 0.2796E+00
Please see towhee_citations for a list of suggested citations for this simulation
