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: /towheebase/Examples/Canonical_Ensemble/AVB1_Methane/
inputformat: Towhee
ensemble: nvt
temperature: 100.000
nmolty: 1
nmolectyp: 500
numboxes: 1
stepstyle: cycles
nstep: 10
printfreq: 1
blocksize: 2
moviefreq: 100
backupfreq: 1000
runoutput: full
Full output of updates and block averages
pdb_output_freq: 5
pressurefreq: 2
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_TraPPE-UA
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: T
rmin: 1.00000
rcut: 20.0000
rcutin: 5.00000
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: F
initboxtype: dimensions
initstyle Box: 1
full cbmc
Box: 1 initlattice: simple cubic
Box: 1 initmol: 500
Box: 1 inix,iniy,iniz: 8 8 8
Box idim hmatrix: 1 1 270.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 270.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 270.00000
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000
pmavb1: 1.00000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 20.0000
pmtracm: 1.00000
pmtcmt: 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 TraPPE-UA force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:CH4 charge: 0.00000
Verifying input structures are consistent
Determining CBMC bond distributions
for molecule type 1
Determining Autofit Gaussian bend A parameters
Determining Autofit Gaussian bend B parameters
Determining Autofit Gaussian dihedral parameters
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 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
Reading in initial conformation from towhee_inital
Initial version: 1
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
new maximum displacements read from towhee_initial
box: 1
molecule type: 1
Max displacement for Atom translate: 0.500000
Max displacement for COM translate: 0.689724
Max displacement for rotation: 0.050000
Max disp. for unit cell perturbation
new box dimensions read from towhee_initial
Box 1 hmatrix(1,x): 270.00000 0.00000 0.00000
Box 1 hmatrix(2,x): 0.00000 270.00000 0.00000
Box 1 hmatrix(3,x): 0.00000 0.00000 270.00000
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
2 CH4 2 CH4 3.7300 148.0000 0.0000 0.0000 0.0000
Number of MC cycles: 10
Number of molecules: 500
Temperature [K]: 100.00000
Initial Energies for Box 1
Total molecules in this box 500
Molecules of type 1 : 500
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 -323515.963 [K] -642.89605 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -323510.662 [K] -642.88551 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -5.301 [K] -0.01053 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -323515.9631 [K] -642.896047 [kcal/mol]
initial virial pressure in box 1 = 8.85
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 -0.3072E+06 0.1968E+08 8.8 500
2 B: 1 -0.2948E+06 0.1968E+08 1.6 500
Block Averages (BA) for block 1
BA Box: 1 Volume [A^3] 0.19683000E+08
BA Box: 1 V^2 [A^6] 0.38742049E+15
BA Box: 1 Specific density [g/ml] 0.67672071E-03
BA Box: 1 Virial Pressure [kPa] 0.15681820E+01
BA Box: 1 Total Classical -.30923622E+06
BA Box: 1 Inter vdw -.30923622E+06
BA Box: 1 Angle 0.00000000E+00
BA Box: 1 Torsion 0.00000000E+00
BA Box: 1 Intra vdw 0.00000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw -.53013435E+01
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.25402632E-01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Stress Tensor Virial S_xx [kPa] 0.15260996E+01
BA Box: 1 Stress Tensor Virial S_yy [kPa] -.89946162E+01
BA Box: 1 Stress Tensor Virial S_zz [kPa] 0.12195374E+02
BA Box: 1 Stress Tensor Virial S_xy [kPa] 0.16953417E+02
BA Box: 1 Stress Tensor Virial S_xz [kPa] 0.32706184E+02
BA Box: 1 Stress Tensor Virial S_yz [kPa] 0.33291016E+02
BA Box: 1 Stress Tensor Virial P_tail [kPa] -.74371396E-02
BA Box: 1 Radius of Gyration Type: 1 0.00000
3 B: 1 -0.2778E+06 0.1968E+08 1.6 500
4 B: 1 -0.2690E+06 0.1968E+08 2.7 500
Block Averages (BA) for block 2
BA Box: 1 Volume [A^3] 0.19683000E+08
BA Box: 1 V^2 [A^6] 0.38742049E+15
BA Box: 1 Specific density [g/ml] 0.67672071E-03
BA Box: 1 Virial Pressure [kPa] 0.26985024E+01
BA Box: 1 Total Classical -.27941293E+06
BA Box: 1 Inter vdw -.27941293E+06
BA Box: 1 Angle 0.00000000E+00
BA Box: 1 Torsion 0.00000000E+00
BA Box: 1 Intra vdw 0.00000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw -.53013435E+01
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.25402632E-01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Stress Tensor Virial S_xx [kPa] 0.41726352E+01
BA Box: 1 Stress Tensor Virial S_yy [kPa] -.31659692E+01
BA Box: 1 Stress Tensor Virial S_zz [kPa] 0.71111527E+01
BA Box: 1 Stress Tensor Virial S_xy [kPa] 0.14728704E+02
BA Box: 1 Stress Tensor Virial S_xz [kPa] 0.31684125E+02
BA Box: 1 Stress Tensor Virial S_yz [kPa] 0.33554192E+02
BA Box: 1 Stress Tensor Virial P_tail [kPa] -.74371396E-02
BA Box: 1 Radius of Gyration Type: 1 0.00000
5 B: 1 -0.2591E+06 0.1968E+08 2.7 500
6 B: 1 -0.2492E+06 0.1968E+08 1.9 500
Block Averages (BA) for block 3
BA Box: 1 Volume [A^3] 0.19683000E+08
BA Box: 1 V^2 [A^6] 0.38742049E+15
BA Box: 1 Specific density [g/ml] 0.67672071E-03
BA Box: 1 Virial Pressure [kPa] 0.19309274E+01
BA Box: 1 Total Classical -.25908102E+06
BA Box: 1 Inter vdw -.25908102E+06
BA Box: 1 Angle 0.00000000E+00
BA Box: 1 Torsion 0.00000000E+00
BA Box: 1 Intra vdw 0.00000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw -.53013435E+01
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.25402632E-01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Stress Tensor Virial S_xx [kPa] 0.11048389E+01
BA Box: 1 Stress Tensor Virial S_yy [kPa] -.21929890E+01
BA Box: 1 Stress Tensor Virial S_zz [kPa] 0.69032438E+01
BA Box: 1 Stress Tensor Virial S_xy [kPa] 0.17121568E+02
BA Box: 1 Stress Tensor Virial S_xz [kPa] 0.31198004E+02
BA Box: 1 Stress Tensor Virial S_yz [kPa] 0.33915861E+02
BA Box: 1 Stress Tensor Virial P_tail [kPa] -.74371396E-02
BA Box: 1 Radius of Gyration Type: 1 0.00000
7 B: 1 -0.2401E+06 0.1968E+08 1.9 500
8 B: 1 -0.2299E+06 0.1968E+08 10.1 500
Block Averages (BA) for block 4
BA Box: 1 Volume [A^3] 0.19683000E+08
BA Box: 1 V^2 [A^6] 0.38742049E+15
BA Box: 1 Specific density [g/ml] 0.67672071E-03
BA Box: 1 Virial Pressure [kPa] 0.10052033E+02
BA Box: 1 Total Classical -.23944798E+06
BA Box: 1 Inter vdw -.23944798E+06
BA Box: 1 Angle 0.00000000E+00
BA Box: 1 Torsion 0.00000000E+00
BA Box: 1 Intra vdw 0.00000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw -.53013435E+01
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.25402632E-01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Stress Tensor Virial S_xx [kPa] 0.60714217E+01
BA Box: 1 Stress Tensor Virial S_yy [kPa] 0.62080321E+01
BA Box: 1 Stress Tensor Virial S_zz [kPa] 0.17898956E+02
BA Box: 1 Stress Tensor Virial S_xy [kPa] 0.19961344E+02
BA Box: 1 Stress Tensor Virial S_xz [kPa] 0.28454292E+02
BA Box: 1 Stress Tensor Virial S_yz [kPa] 0.39651198E+02
BA Box: 1 Stress Tensor Virial P_tail [kPa] -.74371396E-02
BA Box: 1 Radius of Gyration Type: 1 0.00000
9 B: 1 -0.2228E+06 0.1968E+08 10.1 500
10 B: 1 -0.2164E+06 0.1968E+08 12.0 500
Block Averages (BA) for block 5
BA Box: 1 Volume [A^3] 0.19683000E+08
BA Box: 1 V^2 [A^6] 0.38742049E+15
BA Box: 1 Specific density [g/ml] 0.67672071E-03
BA Box: 1 Virial Pressure [kPa] 0.12004132E+02
BA Box: 1 Total Classical -.22257814E+06
BA Box: 1 Inter vdw -.22257814E+06
BA Box: 1 Angle 0.00000000E+00
BA Box: 1 Torsion 0.00000000E+00
BA Box: 1 Intra vdw 0.00000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw -.53013435E+01
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.25402632E-01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Stress Tensor Virial S_xx [kPa] 0.83377351E+01
BA Box: 1 Stress Tensor Virial S_yy [kPa] 0.83108589E+01
BA Box: 1 Stress Tensor Virial S_zz [kPa] 0.19386114E+02
BA Box: 1 Stress Tensor Virial S_xy [kPa] 0.20708312E+02
BA Box: 1 Stress Tensor Virial S_xz [kPa] 0.30358862E+02
BA Box: 1 Stress Tensor Virial S_yz [kPa] 0.38222552E+02
BA Box: 1 Stress Tensor Virial P_tail [kPa] -.74371396E-02
BA Box: 1 Radius of Gyration Type: 1 0.00000
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 270.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 270.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 270.00000
* Aggregation-Volume-Bias-1 Moves *
Box Moved Around From To Attempted Accepted Percent
1 1 1 in in 872 17 1.95
1 1 1 in out 864 144 16.67
1 1 1 out in 1653 9 0.54
1 1 1 out out 1611 421 26.13
Final Energies for Box 1
Total molecules in this box 500
Molecules of type 1 : 500
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 -216371.442 [K] -429.97676 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -216366.141 [K] -429.96622 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -5.301 [K] -0.01053 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -216371.4425 [K] -429.976758 [kcal/mol]
Averages Units Type Box 1
Volume nm^3 0.19683E+05
Volume^2 nm^6 0.38742E+09
Molecule Number 1 500.000
Molar Volume ml/mol 0.23706E+05
Specific Density g/ml 0.00067672
Number Density nm-3 1 0.02540
Mole Fraction 1 1.0000000
Radius of Gyration A 1 0.0000000
Virial Pressure kPa 0.56508E+01
Virial S_xx kPa 0.42425E+01
Virial S_yy kPa 0.33063E-01
Virial S_zz kPa 0.12699E+02
Virial S_xy kPa 0.17895E+02
Virial S_xz kPa 0.30880E+02
Virial S_yz kPa 0.35727E+02
Virial P_tail kPa -.74371E-02
Virial p_i <x_i><p_v> kPa 1 0.56508E+01
Ideal Pressure kPa 0.35083E+02
Ideal p_i <N/V>kT kPa 1 0.35083E+02
Total Classical K -0.2620E+06
Inter vdw K -0.2620E+06
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 -0.5301E+01
Solvation K 0.0000E+00
G: Sum{<u_i><N_i>} kJ/mol 0.0000E+00
U kJ/mol -0.2178E+04
pV: <p><V> kJ/mol 0.6696E+02
H: <U> + <p><V> kJ/mol -0.2111E+04
H: <U + pV> kJ/mol -0.2027E+04
S: (<H> - <G>)/T kJ/K mol -0.2111E+02
Z: <p><V>/<N>RT 0.161070
C_v: T^2<H^2>-<H>^2 J/K mol 0.8034E+06
Block Averages ( 5 blocks) Units Type Box Average Standard Deviation
Specific Density g/ml 1 0.67672E-03 0.00000E+00
Virial Pressure kPa 1 0.56508E+01 0.44488E+01
Virial S_xx kPa 1 0.42425E+01 0.27329E+01
Virial S_yy kPa 1 0.33063E-01 0.63772E+01
Virial S_zz kPa 1 0.12699E+02 0.52312E+01
Virial S_xy kPa 1 0.17895E+02 0.21769E+01
Virial S_xz kPa 1 0.30880E+02 0.14310E+01
Virial S_yz kPa 1 0.35727E+02 0.26669E+01
Virial P_tail kPa 1 -0.74371E-02 0.00000E+00
Total Classical K 1 -0.26195E+06 0.30350E+05
Inter vdw K 1 -0.26195E+06 0.30350E+05
Angle K 1 0.00000E+00 0.00000E+00
Torsion K 1 0.00000E+00 0.00000E+00
Intra vdw K 1 0.00000E+00 0.00000E+00
External Field K 1 0.00000E+00 0.00000E+00
Vibration K 1 0.00000E+00 0.00000E+00
Coulomb K 1 0.00000E+00 0.00000E+00
Tail vdw K 1 -0.53013E+01 0.00000E+00
Solvation K 1 0.00000E+00 0.00000E+00
Number Density nm-3 1 1 0.25403E-01 0.00000E+00
Mole Fraction 1 1 1.0000000 0.0000000
Molarity M 1 1 0.42197E-01 0.00000E+00
Radius of Gyration A 1 1 0.00000 0.00000
-----block averages ------
Box: 1
Block Energy Density Virial Press. Mol fracs
1 -.30923622E+06 0.67672071E-03 0.15681820E+01 1.00000000
2 -.27941293E+06 0.67672071E-03 0.26985024E+01 1.00000000
3 -.25908102E+06 0.67672071E-03 0.19309274E+01 1.00000000
4 -.23944798E+06 0.67672071E-03 0.10052033E+02 1.00000000
5 -.22257814E+06 0.67672071E-03 0.12004132E+02 1.00000000
Please see towhee_citations for a list of suggested citations for this simulation
