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: 250.000
nmolty: 1
nmolectyp: 333
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: 100
volmaxdispfreq: 100
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_EPM
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Geometric
lshift: F
ltailc: T
rmin: 1.00000
rcut: 10.0000
rcutin: 10.0000
electrostatic_form: coulomb
coulombstyle: ewald_fixed_kmax
kalp: 5.60000
kmax: 5
dielect: 1.00000
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
initstyle Box: 2
full cbmc
Box: 1 initlattice: simple cubic
Box: 2 initlattice: simple cubic
Box: 1 initmol: 200
Box: 2 initmol: 133
Box: 1 inix,iniy,iniz: 8 8 8
Box: 2 inix,iniy,iniz: 5 5 6
Box idim hmatrix: 1 1 24.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 24.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 24.00000
Box idim hmatrix: 2 1 55.00000 0.00000 0.00000
Box idim hmatrix: 2 2 0.00000 55.00000 0.00000
Box idim hmatrix: 2 3 0.00000 0.00000 55.00000
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: 0.500000E-01
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000
pmavb1: 0.600000E-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: 0.100000
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: 0.550000
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: 3
nmaxcbmc: 3
lpdbnames: F
using the EPM force field
charge_assignment: bond increment
Building the input file for molecule type: 1
unit: 1 name:O_EPM2
unit: 2 name:C_EPM2
unit: 3 name:O_EPM2
Charges assigned for Molecule Type: 1
Unit: 1 nbname: O_EPM2 Charge: -0.32560
Unit: 2 nbname: C_EPM2 Charge: 0.65120
Unit: 3 nbname: O_EPM2 Charge: -0.32560
Total charge for Molecule Type: 1 is: 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
Type: 2 Style: Fixed Length: 1.1490
Angle Types
Type: 3 Style: Standard Harmonic Angle: 180.000 Constant: 74327.9
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
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 44.0090 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 0.04167 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.04167 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.04167
Box idim hinverse: 2 1 0.01818 0.00000 0.00000
Box idim hinverse: 2 2 0.00000 0.01818 0.00000
Box idim hinverse: 2 3 0.00000 0.00000 0.01818
Box: 1 Initial calp: 0.23333
Box: 1 Initial kmax: 5
Box: 2 Initial calp: 0.10182
Box: 2 Initial kmax: 5
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
5 C_EPM2 5 C_EPM2 2.7570 28.1290 0.0000 0.0000 0.0000
5 C_EPM2 6 O_EPM2 2.8917 47.5876 0.0000 0.0000 0.0000
6 O_EPM2 6 O_EPM2 3.0330 80.5070 0.0000 0.0000 0.0000
Number of MC cycles: 1
Number of molecules: 333
Temperature [K]: 250.00000
Initial Energies for Box 1
Total molecules in this box 200
Molecules of type 1 : 200
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 64828.608 [K] 128.82844 [kcal/mol]
regular 64828.608 [K] 128.82844 [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 1526406062.453 [K] 3033298.31022 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 1526415134.429 [K] 3033316.33819 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -9071.976 [K] -18.02797 [kcal/mol]
total coulombic 25989.831 [K] 51.64740 [kcal/mol]
real space 30700.832 [K] 61.00918 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 30700.832 [K] 61.00918 [kcal/mol]
self -2798518.089 [K] -5561.25948 [kcal/mol]
correction 2793119.705 [K] 5550.53173 [kcal/mol]
recip sum 687.383 [K] 1.36598 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 1526496880.8925 [K] 3033478.786058 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 133
Molecules of type 1 : 133
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 43111.025 [K] 85.67091 [kcal/mol]
regular 43111.025 [K] 85.67091 [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 -704.943 [K] -1.40087 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -371.600 [K] -0.73845 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -333.343 [K] -0.66242 [kcal/mol]
total coulombic 321.552 [K] 0.63899 [kcal/mol]
real space 379.552 [K] 0.75425 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 379.552 [K] 0.75425 [kcal/mol]
self -812079.067 [K] -1613.77639 [kcal/mol]
correction 812013.990 [K] 1613.64707 [kcal/mol]
recip sum 7.077 [K] 0.01406 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 42727.6337 [K] 84.909031 [kcal/mol]
initial virial pressure in box 1 = 9747758154.84
initial virial pressure in box 2 = 2684.99
+++++ 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) 24.98563 0.00000 0.00000
hmatrix(2,x) 0.00000 24.98563 0.00000
hmatrix(3,x) 0.00000 0.00000 24.98563
Box: 2
hmatrix(1,x) 54.80381 0.00000 0.00000
hmatrix(2,x) 0.00000 54.80381 0.00000
hmatrix(3,x) 0.00000 0.00000 54.80381
* 3D Volume Change Moves *
Box 1 and 2 Tries: 2 Accepted: 2 Acp. Ratio: 1.000 Max Disp.: 0.100E+00
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 13 Grown: 13 Accepted: 4
From box 1 to box 2 Attempted: 7 Grown: 7 Accepted: 7
* Aggregation-Volume-Bias-1 Moves *
Box Moved Around From To Attempted Accepted Percent
1 1 1 out in 1 1 100.00
1 1 1 out out 1 1 100.00
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 3 3 1 100.00 33.33
2 5 5 5 100.00 100.00
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
1 1 1 1 100.00 100.00
2 2 2 0 100.00 0.00
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 80. Accepted: 27. Accepted: 33.750 %
Molecule: 1 Box: 2 Attempts: 82. Accepted: 82. Accepted: 100.000 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 73. Accepted: 45. Accepted: 61.644 %
Molecule: 1 Box: 2 Attempts: 63. Accepted: 63. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 197
Molecules of type 1 : 197
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 64895.168 [K] 128.96071 [kcal/mol]
regular 64895.168 [K] 128.96071 [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 550627451.399 [K] 1094215.59503 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 550635252.160 [K] 1094231.09683 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -7800.761 [K] -15.50180 [kcal/mol]
total coulombic 33547.662 [K] 66.66645 [kcal/mol]
real space 37018.975 [K] 73.56469 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 37018.975 [K] 73.56469 [kcal/mol]
self -2647800.298 [K] -5261.75070 [kcal/mol]
correction 2643416.907 [K] 5253.03996 [kcal/mol]
recip sum 912.079 [K] 1.81250 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 550725894.2295 [K] 1094411.222184 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 136
Molecules of type 1 : 136
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 43788.300 [K] 87.01680 [kcal/mol]
regular 43788.300 [K] 87.01680 [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 -1678.874 [K] -3.33629 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -1326.568 [K] -2.63618 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -352.307 [K] -0.70011 [kcal/mol]
total coulombic -80.226 [K] -0.15943 [kcal/mol]
real space -25.844 [K] -0.05136 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. -25.844 [K] -0.05136 [kcal/mol]
self -833369.340 [K] -1656.08476 [kcal/mol]
correction 833301.679 [K] 1655.95030 [kcal/mol]
recip sum 13.279 [K] 0.02639 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 42029.1994 [K] 83.521091 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.14554E+02 0.16564E+03
Volume^2 nm^6 0.21246E+03 0.27439E+05
Molecule Number 1 199.967 133.033
Molar Volume ml/mol 0.43694E+02 0.74980E+03
Specific Density g/ml 1.00722050 0.05869449
Number Density nm-3 1 13.78247 0.80316
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 0.9793451 0.9793540
Ideal Pressure kPa 0.47586E+05 0.27730E+04
Ideal p_i <N/V>kT kPa 1 0.47586E+05 0.27730E+04
-<dU/dV> kPa 0.55445E+10 -.14747E+03
Thermodynamic Pressure kPa 0.55446E+10 0.26256E+04
Thermo p_i <x_1><p_t> kPa 1 0.55446E+10 0.26256E+04
Total Classical K 0.1051E+10 0.4202E+05
Inter vdw K 0.1051E+10 -0.1057E+04
Angle K 0.6527E+05 0.4291E+05
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 0.3135E+05 0.1665E+03
Tail vdw K -0.8642E+04 -0.3350E+03
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -2416.715 -3126.598
u (NVT Insertion) K 1 1152.072 1852.264
u (NpT Insertion) K 1 1163.901 1852.200
u (Den. + NVT Insert) K 1 -1264.643 -1274.334
u (Den. + NpT Insert) K 1 -1252.814 -1274.399
u (Gibbs Total) K 1 -1251.592 -1272.741
G: Sum{<u_i><N_i>} kJ/mol -0.2081E+04 -0.1408E+04
U kJ/mol 0.8740E+07 0.3494E+03
H_vap (pV/n=RT) kJ/mol -0.4366E+05
Please see towhee_citations for a list of suggested citations for this simulation
