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: 265.000
nmolty: 1
nmolectyp: 340
numboxes: 2
stepstyle: cycles
nstep: 1
printfreq: 1
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_Potter1997
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: LB plus manual
mixrule_adjust_total: 1
mixrule_adjust_key: element
mixrule_adjust_keynames: F H
mixrule_adjustments:
2.30000
22.3600
0.00000
0.00000
lshift: F
ltailc: T
rmin: 1.00000
rcut: 12.0000
rcutin: 10.0000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Lorentz-Berthelot Mixing rules plus manual setting of certain specified cross terms
Arithmetic mean of the other sigma terms
Geometric mean of the other 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: 294
Box: 2 initmol: 46
Box: 1 inix,iniy,iniz: 7 7 7
Box: 2 inix,iniy,iniz: 4 4 4
Box idim hmatrix: 1 1 28.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 28.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 28.00000
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: 0.00000
pm2rbswmt: 1.00000
pm2rbswpr: 1.00000
pm2boxcbswap: 0.100000
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pmavb1: 0.110000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 8.00000
pmavb2: 0.120000
pmavb2in: 0.500000
pmavb2mt: 1.00000
moltyp: 1 pmavb2ct: 1.000000
avb2rad: 8.00000
pmavb3: 0.130000
pmavb3mt: 1.00000
moltyp: 1 pmavb3ct: 1.000000
avb3rad: 8.00000
pmcb: 0.400000
pmcbmt: 1.00000
pmall: 0.00000
pmtraat: 0.00000
pmtamt: 1.00000
rmtraa: 0.500000
tatraa: 0.500000
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 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: Martin and Frischknecht
input_style: basic connectivity map
nunit: 5
nmaxcbmc: 5
lpdbnames: F
using the Potter1997 force field
charge_assignment: bond increment
Building the input file for molecule type: 1
unit: 1 name:C
unit: 2 name:F(2)
unit: 3 name:F(2)
unit: 4 name:H(2)
unit: 5 name:H(2)
Charges assigned for Molecule Type: 1
Unit: 1 nbname: C Charge: 0.21400
Unit: 2 nbname: F(2) Charge: -0.20400
Unit: 3 nbname: F(2) Charge: -0.20400
Unit: 4 nbname: H(2) Charge: 0.09700
Unit: 5 nbname: H(2) Charge: 0.09700
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: 1 Style: Fixed Length: 1.3600
Type: 4 Style: Fixed Length: 1.0900
Angle Types
Type: 1 Style: Standard Harmonic Angle: 113.610 Constant: 13969.6
Type: 2 Style: Standard Harmonic Angle: 108.630 Constant: 28769.0
Type: 3 Style: Standard Harmonic Angle: 108.640 Constant: 19429.9
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
Molecular mass for molecule type 1 is 52.0229 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 0.03571 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.03571 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.03571
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
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 C 1 C 3.1500 54.6000 0.0000 0.0000 0.0000
1 C 2 F(2) 3.0625 46.7333 0.0000 0.0000 0.0000
1 C 6 H(2) 2.6600 23.3666 0.0000 0.0000 0.0000
2 F(2) 2 F(2) 2.9750 40.0000 0.0000 0.0000 0.0000
2 F(2) 6 H(2) 2.3000 22.3600 0.0000 0.0000 0.0000
6 H(2) 6 H(2) 2.1700 10.0000 0.0000 0.0000 0.0000
Number of MC cycles: 1
Number of molecules: 340
Temperature [K]: 265.00000
Initial Energies for Box 1
Total molecules in this box 294
Molecules of type 1 : 294
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 272055.609 [K] 540.63322 [kcal/mol]
regular 272055.609 [K] 540.63322 [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 2370117.191 [K] 4709.93443 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 2377413.693 [K] 4724.43416 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -7296.501 [K] -14.49972 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 2642172.8002 [K] 5250.567649 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 46
Molecules of type 1 : 46
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 42566.524 [K] 84.58887 [kcal/mol]
regular 42566.524 [K] 84.58887 [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 -18.153 [K] -0.03607 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -18.153 [K] -0.03607 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 42548.3705 [K] 84.552796 [kcal/mol]
initial virial pressure in box 1 = 13388888.93
initial virial pressure in box 2 = 776.86
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 0.1825E+07 0.2195E+05 13388888.9 278
B: 2 0.5075E+05 0.2160E+06 776.9 62
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 28.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 28.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 28.00000
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
* 3D Volume Change Moves *
Box 1 and 2 Tries: 1 Accepted: 0 Acp. Ratio: 0.000 Max Disp.: 0.100E+00
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 26 Grown: 26 Accepted: 1
From box 1 to box 2 Attempted: 18 Grown: 18 Accepted: 17
* Aggregation-Volume-Bias-2 Moves
Box Moved Around From To Attempted Accepted Percent
1 1 1 in out 3 0 0.00
Box Moved Around From To Attempted Accepted Percent
2 1 1 in out 1 0 0.00
* Aggregation-Volume-Bias-3 Moves
Box Moved Around Attempted Accepted Percent
2 1 1 3 0 0.00
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
3 11 11 7 100.00 63.64
4 51 51 21 100.00 41.18
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
3 3 3 1 100.00 33.33
4 11 11 7 100.00 63.64
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 98. Accepted: 38. Accepted: 38.776 %
Molecule: 1 Box: 2 Attempts: 13. Accepted: 13. Accepted: 100.000 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 88. Accepted: 53. Accepted: 60.227 %
Molecule: 1 Box: 2 Attempts: 13. Accepted: 13. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 278
Molecules of type 1 : 278
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 255411.892 [K] 507.55856 [kcal/mol]
regular 255411.892 [K] 507.55856 [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 1569692.897 [K] 3119.31859 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 1576216.832 [K] 3132.28306 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -6523.934 [K] -12.96447 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 1825104.7888 [K] 3626.877152 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 62
Molecules of type 1 : 62
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 51712.341 [K] 102.76358 [kcal/mol]
regular 51712.341 [K] 102.76358 [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 -959.043 [K] -1.90582 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -926.065 [K] -1.84029 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -32.978 [K] -0.06553 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 50753.2983 [K] 100.857759 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.21952E+02 0.21600E+03
Volume^2 nm^6 0.48189E+03 0.46656E+05
Molecule Number 1 289.250 50.750
Molar Volume ml/mol 0.45703E+02 0.25631E+04
Specific Density g/ml 1.13828148 0.02029704
Number Density nm-3 1 13.17648 0.23495
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 1.0172151 1.0253955
Ideal Pressure kPa 0.48223E+05 0.85989E+03
Ideal p_i <N/V>kT kPa 1 0.48223E+05 0.85989E+03
-<dU/dV> kPa 0.19574E+08 -.11515E+01
Thermodynamic Pressure kPa 0.19622E+08 0.85874E+03
Thermo p_i <x_1><p_t> kPa 1 0.19622E+08 0.85874E+03
Total Classical K 0.2266E+07 0.4517E+05
Inter vdw K 0.1999E+07 -0.2130E+03
Angle K 0.2674E+06 0.4538E+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 0.0000E+00 0.0000E+00
Tail vdw K -0.7065E+04 -0.2231E+02
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -2662.468 -3729.570
u (NVT Insertion) K 1 3484.766 3579.627
u (NpT Insertion) K 1 3484.766 3579.627
u (Den. + NVT Insert) K 1 822.298 -149.943
u (Den. + NpT Insert) K 1 822.298 -149.943
u (Gibbs Total) K 1 822.367 -128.816
G: Sum{<u_i><N_i>} kJ/mol 0.1978E+04 -0.5435E+02
U kJ/mol 0.1884E+05 0.3755E+03
H_vap (pV/n=RT) kJ/mol -0.5541E+02
Please see towhee_citations for a list of suggested citations for this simulation
