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: 10
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: 10000
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_Sum2003
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: T
rmin: 1.00000
rcut: 10.0000
rcutin: 5.00000
electrostatic_form: coulomb
coulombstyle: ewald_fixed_cutoff
ewald_prec: 0.100000E-03
rcelect: 10.0000
dielect: 1.00000
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
Box: 1 initlattice: simple cubic
Box: 1 initmol: 10
Box: 1 inix,iniy,iniz: 3 2 2
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
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 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: 18
nmaxcbmc: 18
lpdbnames: F
using the Sum2003 force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:CHsp3oac charge: 0.20000
unit: 2 name:CH2sp3oac charge: 0.20000
unit: 3 name:Osp3 charge: -0.40000
unit: 4 name:Csp2ac charge: 0.65000
unit: 5 name:CH2sp3cac charge: 0.05000
unit: 6 name:CH3sp3gen charge: 0.00000
unit: 7 name:Osp2 charge: -0.50000
unit: 8 name:Osp3 charge: -0.40000
unit: 9 name:Csp2ac charge: 0.65000
unit: 10 name:CH2sp3cac charge: 0.05000
unit: 11 name:CH3sp3gen charge: 0.00000
unit: 12 name:Osp2 charge: -0.50000
unit: 13 name:CH2sp3oac charge: 0.20000
unit: 14 name:Osp3 charge: -0.40000
unit: 15 name:Csp2ac charge: 0.65000
unit: 16 name:CH2sp3cac charge: 0.05000
unit: 17 name:CH3sp3gen charge: 0.00000
unit: 18 name:Osp2 charge: -0.50000
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: Standard Harmonic Length: 1.5400 Constant: 48250.0
Type: 2 Style: Standard Harmonic Length: 1.4800 Constant: 132298.9
Type: 3 Style: Standard Harmonic Length: 1.6000 Constant: 120271.7
Type: 4 Style: Standard Harmonic Length: 1.4000 Constant: 162366.8
Type: 5 Style: Standard Harmonic Length: 1.2600 Constant: 180407.5
Type: 6 Style: Standard Harmonic Length: 1.5300 Constant: 120271.7
Angle Types
Type: 4 Style: Standard Harmonic Angle: 117.000 Constant: 55505.4
Type: 5 Style: Standard Harmonic Angle: 124.000 Constant: 91406.5
Type: 6 Style: Standard Harmonic Angle: 111.000 Constant: 72163.0
Type: 7 Style: Standard Harmonic Angle: 125.000 Constant: 91406.5
Type: 8 Style: Standard Harmonic Angle: 114.000 Constant: 51957.4
Type: 9 Style: Standard Harmonic Angle: 109.000 Constant: 60135.8
Type: 10 Style: Standard Harmonic Angle: 119.000 Constant: 72163.0
Torsion Types
Type: 5 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 0.00
n: 0 Constant: 0.00000
n: 1 Constant: 6332.30501
n: 2 Constant: 3639.66219
n: 3 Constant: 0.00000
Type: 6 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 180.00
n: 0 Constant: 0.00000
n: 1 Constant: 6263.02851
n: 2 Constant: 4050.63058
n: 3 Constant: 0.00000
Type: 7 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 180.00
n: 0 Constant: 0.00000
n: 1 Constant: 369.95575
n: 2 Constant: 175.47641
n: 3 Constant: 0.00000
Type: 8 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 0.00
n: 0 Constant: 0.00000
n: 1 Constant: 369.95575
n: 2 Constant: 175.47641
n: 3 Constant: 0.00000
Type: 10 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 180.00
n: 0 Constant: 0.00000
n: 1 Constant: 3885.01645
n: 2 Constant: -1889.10759
n: 3 Constant: 0.00000
Type: 11 Style: Sum2003 Cosine Series n: 3
Torsion shift angle [torcoeff(0)]: 180.00
n: 0 Constant: 0.00000
n: 1 Constant: 1035.29879
n: 2 Constant: 5143.78007
n: 3 Constant: 0.00000
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
Coulombic inter- and intra-molecular interactions
with an Ewald sum
including the real-space terms up to half the shortest box length
Molecular mass for molecule type 1 is 260.2840 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: 1 Initial calp: 0.27316
Box: 1 Initial kmax: 7
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 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 CH3sp3gen 1 CH3sp3gen 3.9100 104.0000 0.0000 0.0000 0.0000
1 CH3sp3gen 6 Csp2ac 3.6110 94.8008 0.0000 0.0000 0.0000
1 CH3sp3gen 7 CH2sp3oac 3.8700 89.1010 0.0000 0.0000 0.0000
1 CH3sp3gen 8 CH2sp3cac 3.8725 88.4388 0.0000 0.0000 0.0000
1 CH3sp3gen 10 CHsp3oac 3.8700 89.1010 0.0000 0.0000 0.0000
1 CH3sp3gen 13 Osp3 3.6910 91.7909 0.0000 0.0000 0.0000
1 CH3sp3gen 14 Osp2 3.3750 99.5442 0.0000 0.0000 0.0000
6 Csp2ac 6 Csp2ac 3.3120 86.4152 0.0000 0.0000 0.0000
6 Csp2ac 7 CH2sp3oac 3.5710 81.2196 0.0000 0.0000 0.0000
6 Csp2ac 8 CH2sp3cac 3.5735 80.6160 0.0000 0.0000 0.0000
6 Csp2ac 10 CHsp3oac 3.5710 81.2196 0.0000 0.0000 0.0000
6 Csp2ac 13 Osp3 3.3920 83.6716 0.0000 0.0000 0.0000
6 Csp2ac 14 Osp2 3.0760 90.7391 0.0000 0.0000 0.0000
7 CH2sp3oac 7 CH2sp3oac 3.8300 76.3364 0.0000 0.0000 0.0000
7 CH2sp3oac 8 CH2sp3cac 3.8325 75.7691 0.0000 0.0000 0.0000
7 CH2sp3oac 10 CHsp3oac 3.8300 76.3364 0.0000 0.0000 0.0000
7 CH2sp3oac 13 Osp3 3.6510 78.6409 0.0000 0.0000 0.0000
7 CH2sp3oac 14 Osp2 3.3350 85.2835 0.0000 0.0000 0.0000
8 CH2sp3cac 8 CH2sp3cac 3.8350 75.2059 0.0000 0.0000 0.0000
8 CH2sp3cac 10 CHsp3oac 3.8325 75.7691 0.0000 0.0000 0.0000
8 CH2sp3cac 13 Osp3 3.6535 78.0564 0.0000 0.0000 0.0000
8 CH2sp3cac 14 Osp2 3.3375 84.6496 0.0000 0.0000 0.0000
10 CHsp3oac 10 CHsp3oac 3.8300 76.3364 0.0000 0.0000 0.0000
10 CHsp3oac 13 Osp3 3.6510 78.6409 0.0000 0.0000 0.0000
10 CHsp3oac 14 Osp2 3.3350 85.2835 0.0000 0.0000 0.0000
13 Osp3 13 Osp3 3.4720 81.0150 0.0000 0.0000 0.0000
13 Osp3 14 Osp2 3.1560 87.8581 0.0000 0.0000 0.0000
14 Osp2 14 Osp2 2.8400 95.2792 0.0000 0.0000 0.0000
Number of MC cycles: 0
Number of molecules: 10
Temperature [K]: 336.00000
Initial Energies for Box 1
Total molecules in this box 10
Molecules of type 1 : 10
total vibration 30505.216 [K] 60.62045 [kcal/mol]
regular 30505.216 [K] 60.62045 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 27195.124 [K] 54.04258 [kcal/mol]
regular 27195.124 [K] 54.04258 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 146426.283 [K] 290.98063 [kcal/mol]
regular 146426.283 [K] 290.98063 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -26120.488 [K] -51.90705 [kcal/mol]
intramolecular -19857.448 [K] -39.46104 [kcal/mol]
2-body nonbond -4455.182 [K] -8.85341 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -1807.857 [K] -3.59260 [kcal/mol]
total coulombic -258766.492 [K] -514.22487 [kcal/mol]
real space -59887.682 [K] -119.00975 [kcal/mol]
intramolec. -60022.144 [K] -119.27696 [kcal/mol]
intermolec. 134.462 [K] 0.26720 [kcal/mol]
self -675989.460 [K] -1343.33697 [kcal/mol]
correction 466673.547 [K] 927.38107 [kcal/mol]
recip sum 10437.104 [K] 20.74078 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -80760.3572 [K] -160.488261 [kcal/mol]
initial virial pressure in box 1 = -4317.23
+++++ 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
Final Energies for Box 1
Total molecules in this box 10
Molecules of type 1 : 10
total vibration 30505.216 [K] 60.62045 [kcal/mol]
regular 30505.216 [K] 60.62045 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 27195.124 [K] 54.04258 [kcal/mol]
regular 27195.124 [K] 54.04258 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 146426.283 [K] 290.98063 [kcal/mol]
regular 146426.283 [K] 290.98063 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -26120.488 [K] -51.90705 [kcal/mol]
intramolecular -19857.448 [K] -39.46104 [kcal/mol]
2-body nonbond -4455.182 [K] -8.85341 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -1807.857 [K] -3.59260 [kcal/mol]
total coulombic -258766.492 [K] -514.22487 [kcal/mol]
real space -59887.682 [K] -119.00975 [kcal/mol]
intramolec. -60022.144 [K] -119.27696 [kcal/mol]
intermolec. 134.462 [K] 0.26720 [kcal/mol]
self -675989.460 [K] -1343.33697 [kcal/mol]
correction 466673.547 [K] 927.38107 [kcal/mol]
recip sum 10437.104 [K] 20.74078 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -80760.3572 [K] -160.488261 [kcal/mol]
Please see towhee_citations for a list of suggested citations for this simulation
