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: 300
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_TraPPE-UA
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: T
rmin: 1.00000
rcut: 14.0000
rcutin: 10.0000
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: F
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: 260
Box: 2 initmol: 40
Box: 1 inix,iniy,iniz: 8 8 7
Box: 2 inix,iniy,iniz: 4 4 4
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
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: 0.100000E-01
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
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: 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: 0.670000
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: 5
nmaxcbmc: 5
lpdbnames: F
using the TraPPE-UA force field
charge_assignment: bond increment
Building the input file for molecule type: 1
unit: 1 name:CH3*(sp3)
unit: 2 name:CH2**(sp3)
unit: 3 name:CH2**(sp3)
unit: 4 name:CH2**(sp3)
unit: 5 name:CH3*(sp3)
Charges assigned for Molecule Type: 1
Unit: 1 nbname: CH3*(sp3) Charge: 0.00000
Unit: 2 nbname: CH2**(sp3) Charge: 0.00000
Unit: 3 nbname: CH2**(sp3) Charge: 0.00000
Unit: 4 nbname: CH2**(sp3) Charge: 0.00000
Unit: 5 nbname: CH3*(sp3) Charge: 0.00000
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: 1.5400
Angle Types
Type: 1 Style: Standard Harmonic Angle: 114.000 Constant: 31250.0
Torsion Types
Type: 1 Style: Old UA OPLS Cosine Series
k0: 0.0 k1: 355.0 k2: -68.2 k3: 791.3
with 1-4 vdw and scaled (0.500) 1-4 coulomb
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 72.1498 g/mol
Reading in initial conformation from towhee_inital
Initial version: 1
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
new maximum displacements read from towhee_initial
box: 1
molecule type: 1
Max displacement for Atom translate: 0.500000
Max displacement for COM translate: 0.810971
Max displacement for rotation: 0.565538
box: 2
molecule type: 1
Max displacement for Atom translate: 0.500000
Max displacement for COM translate: 28.000000
Max displacement for rotation: 3.141500
Max disp. for 3D Volume: 0.2414E-01
Max disp. for unit cell perturbation
Boxes 1 and 2 idim 1 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
Boxes 1 and 2 idim 2 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
Boxes 1 and 2 idim 3 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
new box dimensions read from towhee_initial
Box 1 hmatrix(1,x): 33.34340 0.00000 0.00000
Box 1 hmatrix(2,x): 0.00000 33.34340 0.00000
Box 1 hmatrix(3,x): 0.00000 0.00000 33.34340
Box 2 hmatrix(1,x): 110.10989 0.00000 0.00000
Box 2 hmatrix(2,x): 0.00000 110.10989 0.00000
Box 2 hmatrix(3,x): 0.00000 0.00000 110.10989
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
3 CH3*(sp3) 3 CH3*(sp3) 3.7500 98.0000 0.0000 0.0000 0.0000
3 CH3*(sp3) 4 CH2**(sp3) 3.8500 67.1416 0.0000 0.0000 0.0000
4 CH2**(sp3) 4 CH2**(sp3) 3.9500 46.0000 0.0000 0.0000 0.0000
Number of MC cycles: 1
Number of molecules: 300
Temperature [K]: 336.00000
Initial Energies for Box 1
Total molecules in this box 179
Molecules of type 1 : 179
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 89905.394 [K] 178.66142 [kcal/mol]
regular 89905.394 [K] 178.66142 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 120345.103 [K] 239.15170 [kcal/mol]
regular 120345.103 [K] 239.15170 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -434345.354 [K] -863.13797 [kcal/mol]
intramolecular -11600.204 [K] -23.05211 [kcal/mol]
2-body nonbond -408797.227 [K] -812.36833 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -13947.924 [K] -27.71753 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -224094.8571 [K] -445.324850 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 121
Molecules of type 1 : 121
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 63207.375 [K] 125.60670 [kcal/mol]
regular 63207.375 [K] 125.60670 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 83337.071 [K] 165.60875 [kcal/mol]
regular 83337.071 [K] 165.60875 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -18761.627 [K] -37.28340 [kcal/mol]
intramolecular -7084.086 [K] -14.07761 [kcal/mol]
2-body nonbond -11500.561 [K] -22.85410 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -176.980 [K] -0.35170 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 127782.8188 [K] 253.932042 [kcal/mol]
initial virial pressure in box 1 = 10968.31
initial virial pressure in box 2 = 336.32
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 -0.2214E+06 0.3707E+05 10968.3 179
B: 2 0.1277E+06 0.1335E+07 336.3 121
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 33.34340 0.00000 0.00000
hmatrix(2,x) 0.00000 33.34340 0.00000
hmatrix(3,x) 0.00000 0.00000 33.34340
Box: 2
hmatrix(1,x) 110.10989 0.00000 0.00000
hmatrix(2,x) 0.00000 110.10989 0.00000
hmatrix(3,x) 0.00000 0.00000 110.10989
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 1 to box 2 Attempted: 1 Grown: 1 Accepted: 0
* Aggregation-Volume-Bias-1 Moves *
Box Moved Around From To Attempted Accepted Percent
2 1 1 out out 1 1 100.00
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 16 16 12 100.00 75.00
2 15 15 10 100.00 66.67
3 5 5 0 100.00 0.00
4 21 21 2 100.00 9.52
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
1 7 7 7 100.00 100.00
2 5 5 4 100.00 80.00
3 14 14 12 100.00 85.71
4 17 17 16 100.00 94.12
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 59. Accepted: 31. Accepted: 52.542 %
Molecule: 1 Box: 2 Attempts: 32. Accepted: 20. Accepted: 62.500 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 62. Accepted: 14. Accepted: 22.581 %
Molecule: 1 Box: 2 Attempts: 45. Accepted: 37. Accepted: 82.222 %
Final Energies for Box 1
Total molecules in this box 179
Molecules of type 1 : 179
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 90927.327 [K] 180.69222 [kcal/mol]
regular 90927.327 [K] 180.69222 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 121875.346 [K] 242.19262 [kcal/mol]
regular 121875.346 [K] 242.19262 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -434194.223 [K] -862.83764 [kcal/mol]
intramolecular -11077.434 [K] -22.01325 [kcal/mol]
2-body nonbond -409168.866 [K] -813.10685 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -13947.924 [K] -27.71753 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -221391.5508 [K] -439.952797 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 121
Molecules of type 1 : 121
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 63844.399 [K] 126.87260 [kcal/mol]
regular 63844.399 [K] 126.87260 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 82553.663 [K] 164.05195 [kcal/mol]
regular 82553.663 [K] 164.05195 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -18741.971 [K] -37.24434 [kcal/mol]
intramolecular -7722.854 [K] -15.34698 [kcal/mol]
2-body nonbond -10842.136 [K] -21.54567 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -176.980 [K] -0.35170 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical 127656.0914 [K] 253.680207 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.37071E+02 0.13350E+04
Volume^2 nm^6 0.13742E+04 0.17822E+07
Molecule Number 1 179.000 121.000
Molar Volume ml/mol 0.12472E+03 0.66441E+04
Specific Density g/ml 0.57851466 0.01085919
Number Density nm-3 1 4.82862 0.09064
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 1.8000726 1.8107753
Ideal Pressure kPa 0.22407E+05 0.42059E+03
Ideal p_i <N/V>kT kPa 1 0.22407E+05 0.42059E+03
Total Classical K -0.2209E+06 0.1285E+06
Inter vdw K -0.4208E+06 -0.1196E+05
Angle K 0.9046E+05 0.6340E+05
Torsion K 0.1208E+06 0.8457E+05
Intra vdw K -0.1145E+05 -0.7464E+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 -0.1395E+05 -0.1770E+03
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 0.000 -5333.340
u (NVT Insertion) K 1 0.000 3536.847
u (NpT Insertion) K 1 0.000 3536.847
u (Den. + NVT Insert) K 1 0.000 -1796.493
u (Den. + NpT Insert) K 1 0.000 -1796.493
u (Gibbs Total) K 1 0.000 -1793.727
G: Sum{<u_i><N_i>} kJ/mol 0.0000E+00 -0.1804E+04
U kJ/mol -0.1837E+04 0.1069E+04
H_vap (pV/n=RT) kJ/mol 0.2189E+02
Please see towhee_citations for a list of suggested citations for this simulation
