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: 1
nmolectyp: 300
numboxes: 2
stepstyle: cycles
nstep: 1
printfreq: 1000
blocksize: 2000
moviefreq: 100000
backupfreq: 1000
runoutput: full
Full output of updates and block averages
pdb_output_freq: 10
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_Gordon
classical_potential: Gordon n-6
READCLASSICAL: pot_num: 13 potential name: Gordon n-6
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: T
rmin: 1.00000
rcut: 14.0000
rcutin: 10.0000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Lorentz-Berthelot Mixing rules
Arithmetic mean of sigma terms
Geometric mean of epsilon term
default max_bond_length: 3.00
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
full cbmc
initstyle Box: 2
full cbmc
Box: 1 initlattice: simple cubic
Box: 2 initlattice: simple cubic
Box: 1 initmol: 260
Box: 2 initmol: 40
Box: 1 inix,iniy,iniz: 8 8 7
Box: 2 inix,iniy,iniz: 4 4 4
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
Box idim hmatrix: 2 1 60.00000 0.00000 0.00000
Box idim hmatrix: 2 2 0.00000 60.00000 0.00000
Box idim hmatrix: 2 3 0.00000 0.00000 60.00000
itest: 1 pairbox: 1 2
pmvol: 0.200000E-02
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pmcell: 0.00000
pmcellpr: 1.00000
pairbox: 1 2 pmcellpt: 0.500000
rmcell: 1.00000
tacell: 0.500000
pm2boxrbswap: 0.00000
pm2rbswmt: 1.00000
pm2rbswpr: 1.00000
pm2boxcbswap: 0.100000E-01
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000
pmavb1: 0.200000E-01
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 8.00000
pmavb2: 0.00000
pmavb2in: 0.500000
pmavb2mt: 1.00000
moltyp: 1 pmavb2ct: 1.000000
avb2rad: 8.00000
pmavb3: 0.00000
pmavb3mt: 1.00000
moltyp: 1 pmavb3ct: 1.000000
avb3rad: 8.00000
pmcb: 0.00000
pmcbmt: 1.00000
pmall: 0.00000
pmback: 0.00000
pmbkmt: 1.00000
pmpivot: 0.00000
pmpivmt: 1.00000
pmconrot: 0.00000
pmcrmt: 1.00000
pmcrback: 0.00000
pmcrbmt: 1.00000
pmplane: 0.00000
pmplanebox: 0.500000 1.00000
planewidth: 3.00000
pmrow: 0.00000
pmrowbox: 0.500000 1.00000
rowwidth: 3.00000
pmtraat: 0.00000
pmtamt: 1.00000
rmtraa: 0.500000
tatraa: 0.500000
pmtracm: 0.670000
pmtcmt: 1.00000
rmtrac: 0.500000
tatrac: 0.500000
pmrotate: 1.00000
pmromt: 1.00000
rmrot: 0.500000E-01
tarot: 0.500000
cbmc_formulation: Martin and Siepmann 1999 + Martin and Thompson 2004
Original Coupled-Decoupled formulation from
M.G. Martin; J.I. Siepmann; J. Phys. Chem. B103 2977-2980 (1999)
with a decoupled bond length selection from
M.G. Martin; A.P. Thompson; Fluid Phase Equilib. 217 105-110 (2004)
cbmc_setting_style: default ideal
input_style: basic connectivity map
nunit: 1
nmaxcbmc: 1
lpdbnames: F
using the Gordon force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:CH4_3 charge: 0.00000
Verifying input structures are consistent
Determining CBMC bond distributions
for molecule type 1
Determining cyclic subunits for molecule type 1
Default total charge on molecule 1 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 Gibbs 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 16.0426 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
Box idim hinverse: 2 1 0.01667 0.00000 0.00000
Box idim hinverse: 2 2 0.00000 0.01667 0.00000
Box idim hinverse: 2 3 0.00000 0.00000 0.01667
INITCONF: building template for molecule type: 1
Initial Structure Growth Trial: 1
Finished initconf
Energies exclusively from internal potentials
Nonbonded Force Field
Modified n-6 potential of Peter Gordon
with tail corrections
u(r) = 4*epsilon*c(n)[{sigma/(r-a(n)}^n - {sigma/(r-a(n)}^n] - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift
1 CH4_3 1 CH4_3 3.730 148.000 0.000
Number of MC cycles: 1
Number of molecules: 300
Temperature [K]: 336.00000
Initial Energies for Box 1
Total molecules in this box 260
Molecules of type 1 : 260
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 -141991.198 [K] -282.16716 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -138944.844 [K] -276.11340 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -3046.354 [K] -6.05376 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -141991.1982 [K] -282.167159 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 40
Molecules of type 1 : 40
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 -9.013 [K] -0.01791 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -9.013 [K] -0.01791 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -9.01288136 [K] -0.0179105406 [kcal/mol]
initial virial pressure in box 1 = 222297.97
initial virial pressure in box 2 = 857.93
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 30.75827 0.00000 0.00000
hmatrix(2,x) 0.00000 30.75827 0.00000
hmatrix(3,x) 0.00000 0.00000 30.75827
Box: 2
hmatrix(1,x) 59.80497 0.00000 0.00000
hmatrix(2,x) 0.00000 59.80497 0.00000
hmatrix(3,x) 0.00000 0.00000 59.80497
* 3D Volume Change Moves *
Box 1 and 2 Tries: 1 Accepted: 1 Acp. Ratio: 1.000 Max Disp.: 0.100E+00
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 2 Grown: 2 Accepted: 0
From box 1 to box 2 Attempted: 3 Grown: 3 Accepted: 3
* Aggregation-Volume-Bias-1 Moves *
Box Moved Around From To Attempted Accepted Percent
1 1 1 out in 1 0 0.00
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 168. Accepted: 106. Accepted: 63.095 %
Molecule: 1 Box: 2 Attempts: 20. Accepted: 20. Accepted: 100.000 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 89. Accepted: 89. Accepted: 100.000 %
Molecule: 1 Box: 2 Attempts: 16. Accepted: 16. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 257
Molecules of type 1 : 257
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 -149743.539 [K] -297.57273 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -146981.830 [K] -292.08462 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -2761.708 [K] -5.48811 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -149743.5386 [K] -297.572732 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 43
Molecules of type 1 : 43
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 -30.250 [K] -0.06011 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -19.732 [K] -0.03921 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -10.518 [K] -0.02090 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -30.24965764 [K] -0.0601125989 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.27420E+02 0.21558E+03
Volume^2 nm^6 0.75256E+03 0.46475E+05
Molecule Number 1 258.627 41.373
Molar Volume ml/mol 0.63783E+02 0.31376E+04
Specific Density g/ml 0.25151726 0.00511308
Number Density nm-3 1 9.44141 0.19193
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 0.0000000 0.0000000
Ideal Pressure kPa 0.43812E+05 0.89065E+03
Ideal p_i <N/V>kT kPa 1 0.43812E+05 0.89065E+03
-<dU/dV> kPa 0.13046E+06 -.31258E+01
Thermodynamic Pressure kPa 0.17427E+06 0.88752E+03
Thermo p_i <x_1><p_t> kPa 1 0.17427E+06 0.88752E+03
Total Classical K -0.1403E+06 -0.1464E+02
Inter vdw K -0.1403E+06 -0.1464E+02
Angle K 0.0000E+00 0.0000E+00
Torsion K 0.0000E+00 0.0000E+00
Intra vdw K 0.0000E+00 0.0000E+00
External Field K 0.0000E+00 0.0000E+00
Vibration K 0.0000E+00 0.0000E+00
Coulomb K 0.0000E+00 0.0000E+00
Tail vdw K -0.2971E+04 -0.9671E+01
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -3014.855 -4323.512
u (NVT Insertion) K 1 221.751 -16.266
u (NpT Insertion) K 1 210.944 -16.920
u (Den. + NVT Insert) K 1 -2793.104 -4339.778
u (Den. + NpT Insert) K 1 -2803.911 -4340.432
u (Gibbs Total) K 1 -2803.350 -4335.609
G: Sum{<u_i><N_i>} kJ/mol -0.6028E+04 -0.1491E+04
U kJ/mol -0.1166E+04 -0.1217E+00
H_vap (pV/n=RT) kJ/mol 0.7300E+01
Please see towhee_citations for a list of suggested citations for this simulation
