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: /towheebase/Examples/Gibbs_Ensemble/MM2_Ethane/
inputformat: Towhee
ensemble: nvt
temperature: 256.000
nmolty: 1
nmolectyp: 240
numboxes: 2
stepstyle: cycles
nstep: 1
printfreq: 10
blocksize: 20
moviefreq: 5
backupfreq: 1000
runoutput: updates
Output maximum displacement updates
pdb_output_freq: 5
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_MM2
classical_potential: Exponential-6
READCLASSICAL: pot_num: 8 potential name: Exponential-6
classical_mixrule: Explicit
lshift: F
ltailc: F
rcut: 10.0000
rcutin: 5.00000
electrostatic_form: none
Setting up force field parameters from files
opening forcefield file: 1
Explicit declaration of Cross Terms
Please check the forcefield file carefully
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: 150
Box: 2 initmol: 90
Box: 1 inix,iniy,iniz: 6 6 6
Box: 2 inix,iniy,iniz: 4 5 5
Box idim hmatrix: 1 1 22.60000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 22.60000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 22.60000
Box idim hmatrix: 2 1 120.00000 0.00000 0.00000
Box idim hmatrix: 2 2 0.00000 120.00000 0.00000
Box idim hmatrix: 2 3 0.00000 0.00000 120.00000
itest: 1 pairbox: 1 2
pmvol: 0.200000E-01
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pm2boxcbswap: 0.400000
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pmavb1: 0.410000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 8.00000
pmcb: 0.600000
pmcbmt: 1.00000
pmall: 0.00000
pmtracm: 0.800000
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: 8
nmaxcbmc: 8
lpdbnames: F
using the MM2 force field
charge_assignment: none
Building the input file for molecule type: 1
unit: 1 name:Cchhh(sp3)
unit: 2 name:Cchhh(sp3)
unit: 3 name:H
unit: 4 name:H
unit: 5 name:H
unit: 6 name:H
unit: 7 name:H
unit: 8 name:H
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: MM2 Triplet Length: 1.5230 Constant: 159286.170
Type: 2 Style: MM2 Triplet Length: 1.1130 Constant: 166526.450
Angle Types
Type: 3 Style: MM2 Angle: 110.000
Constants: 3.970 0.000
Angle-Bond Logical T Atom A: Cwild Atom B: H
Angle-Bond Constant: 113.733
Type: 5 Style: MM2 Angle: 109.000
Constants: 3.529 0.000
Angle-Bond Logical F Atom A: H Atom B: H
Angle-Bond Constant: 0.000
Torsion Types
Type: 3 Style: OPLS Cosine Series
k1: 0.0 k2: 0.0 k3: 59.6
with 1-4 vdw and scaled (1.000) 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 30.0694 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: 0.938747
Max displacement for rotation: 1.343379
box: 2
molecule type: 1
Max displacement for Atom translate: 0.500000
Max displacement for COM translate: 12.594165
Max displacement for rotation: 3.141500
Max disp. for 3D Volume: 0.4144E-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): 22.92051 0.00000 0.00000
Box 1 hmatrix(2,x): 0.00000 22.92051 0.00000
Box 1 hmatrix(3,x): 0.00000 0.00000 22.92051
Box 2 hmatrix(1,x): 50.67514 0.00000 0.00000
Box 2 hmatrix(2,x): 0.00000 50.67514 0.00000
Box 2 hmatrix(3,x): 0.00000 0.00000 50.67514
Energies exclusively from internal potentials
Nonbonded Force Field
Exponential-6 potential
u(r) = infinity for r < expmin
u(r) = A/r^6 + B exp(C r) - S for r > expmin
Num. Atom(i) Num. Atom(j) A B C S expmin
2 Cchhh(sp3) 2 Cchhh(sp3) -0.1500E+06 0.6421E+07 -0.3289E+01 0.0000E+00 1.040
2 Cchhh(sp3) 3 H -0.7231E+05 0.6713E+07 -0.3743E+01 0.0000E+00 0.910
3 H 3 H -0.3879E+05 0.6859E+07 -0.4167E+01 0.0000E+00 0.820
Number of MC cycles: 1
Number of molecules: 240
Temperature [K]: 256.00000
Initial Energies for Box 1
Total molecules in this box 102
Molecules of type 1 : 102
total vibration 149177.271 [K] 296.44744 [kcal/mol]
regular 149177.271 [K] 296.44744 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 28.068 [K] 0.05578 [kcal/mol]
regular 28.068 [K] 0.05578 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 35026.659 [K] 69.60553 [kcal/mol]
regular 35026.659 [K] 69.60553 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -142497.755 [K] -283.17380 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -142497.755 [K] -283.17380 [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 41734.2431 [K] 82.934949 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 138
Molecules of type 1 : 138
total vibration 208599.827 [K] 414.53288 [kcal/mol]
regular 208599.827 [K] 414.53288 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 40.240 [K] 0.07996 [kcal/mol]
regular 40.240 [K] 0.07996 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 47019.853 [K] 93.43860 [kcal/mol]
regular 47019.853 [K] 93.43860 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -26933.109 [K] -53.52190 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -26933.109 [K] -53.52190 [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 228726.8110 [K] 454.529542 [kcal/mol]
initial virial pressure in box 1 = 50746.35
initial virial pressure in box 2 = 4631.64
+++++ 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) 23.19361 0.00000 0.00000
hmatrix(2,x) 0.00000 23.19361 0.00000
hmatrix(3,x) 0.00000 0.00000 23.19361
Box: 2
hmatrix(1,x) 50.61854 0.00000 0.00000
hmatrix(2,x) 0.00000 50.61854 0.00000
hmatrix(3,x) 0.00000 0.00000 50.61854
* 3D Volume Change Moves *
Box 1 and 2 Tries: 2 Accepted: 1 Acp. Ratio: 0.500 Max Disp.: 0.414E-01
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 51 Grown: 51 Accepted: 6
From box 1 to box 2 Attempted: 40 Grown: 40 Accepted: 0
* Aggregation-Volume-Bias-1 Moves *
Box Moved Around From To Attempted Accepted Percent
2 1 1 out in 1 0 0.00
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
3 3 3 3 100.00 100.00
7 15 15 0 100.00 0.00
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
3 3 3 3 100.00 100.00
6 2 2 1 100.00 50.00
7 32 32 4 100.00 12.50
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 18. Accepted: 5. Accepted: 27.778 %
Molecule: 1 Box: 2 Attempts: 20. Accepted: 11. Accepted: 55.000 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 24. Accepted: 10. Accepted: 41.667 %
Molecule: 1 Box: 2 Attempts: 29. Accepted: 25. Accepted: 86.207 %
Final Energies for Box 1
Total molecules in this box 108
Molecules of type 1 : 108
total vibration 155667.046 [K] 309.34402 [kcal/mol]
regular 155667.046 [K] 309.34402 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 207.714 [K] 0.41277 [kcal/mol]
regular 207.714 [K] 0.41277 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 38438.038 [K] 76.38468 [kcal/mol]
regular 38438.038 [K] 76.38468 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -159928.747 [K] -317.81294 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -159928.747 [K] -317.81294 [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 34384.0514 [K] 68.328532 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 132
Molecules of type 1 : 132
total vibration 193092.285 [K] 383.71605 [kcal/mol]
regular 193092.285 [K] 383.71605 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 216.365 [K] 0.42996 [kcal/mol]
regular 216.365 [K] 0.42996 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 47825.939 [K] 95.04046 [kcal/mol]
regular 47825.939 [K] 95.04046 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -25044.915 [K] -49.76965 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond -25044.915 [K] -49.76965 [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 216089.6746 [K] 429.416825 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.12390E+02 0.12978E+03
Volume^2 nm^6 0.15354E+03 0.16844E+05
Molecule Number 1 104.475 135.525
Molar Volume ml/mol 0.71413E+02 0.57670E+03
Specific Density g/ml 0.42106076 0.05214051
Number Density nm-3 1 8.43265 1.04423
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 0.9732489 0.9731823
Ideal Pressure kPa 0.29814E+05 0.36919E+04
Ideal p_i <N/V>kT kPa 1 0.29814E+05 0.36919E+04
-<dU/dV> kPa -.15794E+05 0.59846E+03
Thermodynamic Pressure kPa 0.14019E+05 0.42903E+04
Thermo p_i <x_1><p_t> kPa 1 0.14019E+05 0.42903E+04
Total Classical K 0.3887E+05 0.2217E+06
Inter vdw K -0.1494E+06 -0.2635E+05
Angle K 0.1158E+03 0.1210E+03
Torsion K 0.3649E+05 0.4708E+05
Intra vdw K 0.0000E+00 0.0000E+00
External Field K 0.0000E+00 0.0000E+00
Vibration K 0.1517E+06 0.2009E+06
Coulomb K 0.0000E+00 0.0000E+00
Tail vdw K 0.0000E+00 0.0000E+00
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -2462.543 -2997.274
u (NVT Insertion) K 1 8142.613 9126.139
u (NpT Insertion) K 1 8140.819 9126.234
u (Den. + NVT Insert) K 1 5680.069 6128.864
u (Den. + NpT Insert) K 1 5678.276 6128.960
u (Gibbs Total) K 1 5679.175 6126.284
G: Sum{<u_i><N_i>} kJ/mol 0.4933E+04 0.6903E+04
U kJ/mol 0.3231E+03 0.1843E+04
H_vap (pV/n=RT) kJ/mol 0.1263E+02
Please see towhee_citations for a list of suggested citations for this simulation
