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: 400.000
pressure: 100.000
nmolty: 1
nmolectyp: 64
numboxes: 1
stepstyle: cycles
nstep: 0
printfreq: 1000
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_SMMKmain
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Geometric
lshift: T
ltailc: F
rmin: 2.00000
rcut: 13.8000
rcutin: 5.00000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Geometric Mixing rules
Geometric mean of all nonbond coefficients
default max_bond_length: 3.00
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
full cbmc
Box: 1 initlattice: simple cubic
Box: 1 initmol: 64
Box: 1 inix,iniy,iniz: 4 4 4
Box idim hmatrix: 1 1 40.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 40.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 40.00000
pmvol: 0.200000E-02
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pmcell: 0.00000
pmcellpr: 1.00000
rmcell: 1.00000
tacell: 0.500000
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: 0.330000
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: 1.00000
planewidth: 3.00000
pmrow: 0.00000
pmrowbox: 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: 16
nmaxcbmc: 16
lpdbnames: F
using the SMMKmain force field
charge_assignment: none
Building the input file for molecule type: 1
unit: 1 name:CH3methyl
unit: 2 name:C
unit: 3 name:CH2
unit: 4 name:C
unit: 5 name:CH2
unit: 6 name:CH
unit: 7 name:CH2
unit: 8 name:C
unit: 9 name:CH3methyl
unit: 10 name:CH3methyl
unit: 11 name:CH3methyl
unit: 12 name:CH3methyl
unit: 13 name:CH3methyl
unit: 14 name:CH3methyl
unit: 15 name:CH3methyl
unit: 16 name:CH3methyl
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
Type: 1 Style: Standard Harmonic Length: 1.5400 Constant: 226450.0
Angle Types
Type: 1 Style: Standard Harmonic Angle: 114.000 Constant: 31250.0
Type: 2 Style: Standard Harmonic Angle: 112.000 Constant: 31250.0
Torsion Types
Type: 2 Style: Old UA OPLS Cosine Series
k0: -251.1 k1: 428.7 k2: -111.8 k3: 441.3
Type: 3 Style: Old UA OPLS Cosine Series
k0: 0.0 k1: 0.0 k2: 0.0 k3: 461.3
Improper Torsion Types
No Improper Types
Special One-Five Types
Type: 1 Atom(i): CH3methyl Atom(j): CH3methyl Sigma: 3.620 Epsilon: 40.000 Shift: -0.0521
Isobaric-isothermal 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 226.2846 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 0.02500 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.02500 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.02500
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
with a shift to zero at the cut-off
u(r) = 4*epsilon[(sigma/r)^12 - (sigma/r)^6] - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4sig 1-4eps
3 CH3methyl 3 CH3methyl 3.9300 78.0000 -0.1663 0.0000 0.0000
3 CH3methyl 4 CH2 3.9300 60.5475 -0.1291 0.0000 0.0000
3 CH3methyl 5 CH 3.8898 49.9600 -0.1002 0.0000 0.0000
3 CH3methyl 6 C 0.0000 0.0000 0.0000 0.0000 0.0000
4 CH2 4 CH2 3.9300 47.0000 -0.1002 0.0000 0.0000
4 CH2 5 CH 3.8898 38.7814 -0.0778 0.0000 0.0000
4 CH2 6 C 0.0000 0.0000 0.0000 0.0000 0.0000
5 CH 5 CH 3.8500 32.0000 -0.0603 0.0000 0.0000
5 CH 6 C 0.0000 0.0000 0.0000 0.0000 0.0000
6 C 6 C 0.0000 0.0000 0.0000 0.0000 0.0000
Number of MC cycles: 0
Number of molecules: 64
Temperature [K]: 400.00000
External pressure [kPa]: 100.00000
Initial Energies for Box 1
Total molecules in this box 64
Molecules of type 1 : 64
total vibration 173621.952 [K] 345.02429 [kcal/mol]
regular 173621.952 [K] 345.02429 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 362266.047 [K] 719.90083 [kcal/mol]
regular 362266.047 [K] 719.90083 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 117984.897 [K] 234.46146 [kcal/mol]
regular 117984.897 [K] 234.46146 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 3875997.901 [K] 7702.44444 [kcal/mol]
intramolecular 1974073.206 [K] 3922.90955 [kcal/mol]
2-body nonbond 1901924.695 [K] 3779.53489 [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 4529870.7972 [K] 9001.831015 [kcal/mol]
initial virial pressure in box 1 = 6642045.82
+++++ 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) 40.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 40.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 40.00000
Final Energies for Box 1
Total molecules in this box 64
Molecules of type 1 : 64
total vibration 173621.952 [K] 345.02429 [kcal/mol]
regular 173621.952 [K] 345.02429 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 362266.047 [K] 719.90083 [kcal/mol]
regular 362266.047 [K] 719.90083 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 117984.897 [K] 234.46146 [kcal/mol]
regular 117984.897 [K] 234.46146 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 3875997.901 [K] 7702.44444 [kcal/mol]
intramolecular 1974073.206 [K] 3922.90955 [kcal/mol]
2-body nonbond 1901924.695 [K] 3779.53489 [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 4529870.7972 [K] 9001.831015 [kcal/mol]
Please see towhee_citations for a list of suggested citations for this simulation
