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: 475.000
nmolty: 1
nmolectyp: 100
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: 10000
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_SKS
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: F
rmin: 1.00000
rcut: 13.8000
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: 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: 80
Box: 2 initmol: 20
Box: 1 inix,iniy,iniz: 5 5 4
Box: 2 inix,iniy,iniz: 3 3 3
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
pm2boxrbswap: 0.100000
pm2rbswmt: 1.00000
pm2rbswpr: 1.00000
pm2boxcbswap: 0.200000
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pmcb: 0.400000
pmcbmt: 1.00000
pmall: 0.00000
pmtracm: 0.700000
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 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: 5
nmaxcbmc: 5
lpdbnames: F
using the SKS force field
charge_assignment: none
Building the input file for molecule type: 1
unit: 1 name:CH3
unit: 2 name:CH2
unit: 3 name:CH2
unit: 4 name:CH2
unit: 5 name:CH3
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
Type: 1 Style: Fixed Length: 1.5400
Angle Types
Type: 1 Style: Standard Harmonic Angle: 114.000 Constant: 31250.0
Torsion Types
Type: 1 Style: OPLS Cosine Series
k1: 177.5 k2: -34.1 k3: 395.6
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 72.0998 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
Lennard-Jones 12-6 potential
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 CH3 1 CH3 3.9300 114.0000 0.0000 0.0000 0.0000
1 CH3 2 CH2 3.9300 73.1984 0.0000 0.0000 0.0000
2 CH2 2 CH2 3.9300 47.0000 0.0000 0.0000 0.0000
Number of MC cycles: 1
Number of molecules: 100
Temperature [K]: 475.00000
Initial Energies for Box 1
Total molecules in this box 80
Molecules of type 1 : 80
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 14272.641 [K] 28.36282 [kcal/mol]
regular 14272.641 [K] 28.36282 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 85656.966 [K] 170.21888 [kcal/mol]
regular 85656.966 [K] 170.21888 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 3418234.059 [K] 6792.76888 [kcal/mol]
intramolecular -6759.762 [K] -13.43311 [kcal/mol]
2-body nonbond 3424993.820 [K] 6806.20198 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 3518163.6655 [K] 6991.350575 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 20
Molecules of type 1 : 20
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 3568.160 [K] 7.09070 [kcal/mol]
regular 3568.160 [K] 7.09070 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 21414.241 [K] 42.55472 [kcal/mol]
regular 21414.241 [K] 42.55472 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -1689.940 [K] -3.35828 [kcal/mol]
intramolecular -1689.940 [K] -3.35828 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 23292.4613 [K] 46.287148 [kcal/mol]
initial virial pressure in box 1 = 15558610.86
initial virial pressure in box 2 = 607.24
+++++ 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) 30.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 30.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 30.00000
Box: 2
hmatrix(1,x) 60.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 60.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 60.00000
* Rotational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 9 Accepted: 2
From box 1 to box 2 Attempted: 4 Accepted: 4
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 6 Grown: 6 Accepted: 2
From box 1 to box 2 Attempted: 4 Grown: 4 Accepted: 4
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 5 5 2 100.00 40.00
2 2 2 2 100.00 100.00
3 2 2 1 100.00 50.00
4 9 9 9 100.00 100.00
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
1 2 2 2 100.00 100.00
2 1 1 1 100.00 100.00
3 1 1 1 100.00 100.00
4 4 4 4 100.00 100.00
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 11. Accepted: 7. Accepted: 63.636 %
Molecule: 1 Box: 2 Attempts: 7. Accepted: 7. Accepted: 100.000 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 23. Accepted: 12. Accepted: 52.174 %
Molecule: 1 Box: 2 Attempts: 10. Accepted: 10. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 76
Molecules of type 1 : 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 20116.407 [K] 39.97564 [kcal/mol]
regular 20116.407 [K] 39.97564 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 76463.573 [K] 151.94962 [kcal/mol]
regular 76463.573 [K] 151.94962 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 1911384.829 [K] 3798.33421 [kcal/mol]
intramolecular -6492.981 [K] -12.90295 [kcal/mol]
2-body nonbond 1917877.809 [K] 3811.23717 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 2007964.8090 [K] 3990.259481 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 24
Molecules of type 1 : 24
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 10286.204 [K] 20.44091 [kcal/mol]
regular 10286.204 [K] 20.44091 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 20454.106 [K] 40.64672 [kcal/mol]
regular 20454.106 [K] 40.64672 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -2112.437 [K] -4.19787 [kcal/mol]
intramolecular -2033.746 [K] -4.04149 [kcal/mol]
2-body nonbond -78.690 [K] -0.15637 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 28627.8732 [K] 56.889763 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.27000E+02 0.21600E+03
Volume^2 nm^6 0.72900E+03 0.46656E+05
Molecule Number 1 76.000 24.000
Molar Volume ml/mol 0.21394E+03 0.54198E+04
Specific Density g/ml 0.33700775 0.01330294
Number Density nm-3 1 2.81481 0.11111
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 1.6938436 1.7126930
Ideal Pressure kPa 0.18465E+05 0.72889E+03
Ideal p_i <N/V>kT kPa 1 0.18465E+05 0.72889E+03
Total Classical K 0.2585E+07 0.2926E+05
Inter vdw K 0.2496E+07 -0.1103E+03
Angle K 0.1652E+05 0.8462E+04
Torsion K 0.7900E+05 0.2290E+05
Intra vdw K -0.6520E+04 -0.1989E+04
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 0.0000E+00 0.0000E+00
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -6153.869 -7689.127
u (NVT Insertion) K 1 3219.625 4358.384
u (NpT Insertion) K 1 3219.625 4358.384
u (Den. + NVT Insert) K 1 -2934.244 -3330.742
u (Den. + NpT Insert) K 1 -2934.244 -3330.742
u (Gibbs Total) K 1 -2938.366 -3356.663
G: Sum{<u_i><N_i>} kJ/mol -0.1857E+04 -0.6698E+03
U kJ/mol 0.2149E+05 0.2433E+03
H_vap (pV/n=RT) kJ/mol -0.2680E+03
Please see towhee_citations for a list of suggested citations for this simulation
