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: npt
temperature: 298.000
pressure: 101.325
nmolty: 1
nmolectyp: 180
numboxes: 1
stepstyle: cycles
nstep: 1
printfreq: 1000
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_Gromos43A1
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Explicit
lshift: T
ltailc: F
rmin: 1.00000
rcut: 14.0000
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
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
template
Box: 1 initlattice: simple cubic
Box: 1 initmol: 180
Box: 1 inix,iniy,iniz: 8 8 5
Box idim hmatrix: 1 1 32.60000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 32.60000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 32.60000
pmvol: 0.100000E-01
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pmcb: 0.330000
pmcbmt: 1.00000
pmall: 0.00000
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: explicit
nunit: 5
nmaxcbmc: 5
bead: 1 beadtype: 14 charge: 0.00000
bead: 2 beadtype: 13 charge: 0.00000
bead: 3 beadtype: 13 charge: 0.00000
bead: 4 beadtype: 20 charge: 0.00000
bead: 5 beadtype: 14 charge: 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: 26 Style: Gromos Length: 1.5300 Constant: 21498.6
Type: 29 Style: Gromos Length: 1.7800 Constant: 17860.3
Type: 30 Style: Gromos Length: 1.8300 Constant: 16898.2
Angle Types
Type: 3 Style: Harmonic Cosine Angle: 100.000 Constant: 28564.5
Type: 14 Style: Harmonic Cosine Angle: 111.000 Constant: 31872.0
Type: 15 Style: Harmonic Cosine Angle: 113.000 Constant: 32774.0
Torsion Types
Type: 13 Style: Amber/Charmm/Gromos Cosine Series n: 1
Index 1 k: 352.4 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (1.000) 1-4 coulomb
Type: 17 Style: Amber/Charmm/Gromos Cosine Series n: 1
Index 1 k: 704.8 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (1.000) 1-4 coulomb
Improper Torsion Types
No Improper Types
Isobaric-isothermal 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 90.1890 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: 0.594713
Max displacement for COM translate: 0.594604
Max displacement for rotation: 0.362834
Max disp. for 3D Volume: 0.6012E+03
Max disp. for unit cell perturbation
Box 1 idim 1 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
Box 1 idim 2 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
Box 1 idim 3 rmcell: 0.1000E+01 0.1000E+01 0.1000E+01
new box dimensions read from towhee_initial
Box 1 hmatrix(1,x): 32.21229 0.00000 0.00000
Box 1 hmatrix(2,x): 0.00000 32.21229 0.00000
Box 1 hmatrix(3,x): 0.00000 0.00000 32.21229
Box: 1 Initial calp: 0.17385
Box: 1 Initial kmax: 5
Energies exclusively from internal potentials
Nonbonded Force Field
Lennard-Jones 12-6 potential
with a shift to zero at the cut-off
u(r) = 4*epsilon[(sigma/r)^12 - (sigma/r)^6] - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4sig 1-4eps
13 CH2 13 CH2 3.9199 58.8835 -0.1134 3.3855 94.3285
13 CH2 14 CH3 3.8974 72.0135 -0.1340 3.4299 105.0798
13 CH2 20 S 3.6008 116.1783 -0.1345 3.3464 147.0448
14 CH3 14 CH3 3.8750 88.0714 -0.1583 3.4748 117.0565
14 CH3 20 S 3.5801 142.0842 -0.1589 3.3902 163.8045
20 S 20 S 3.3077 229.2220 -0.1595 3.3077 229.2220
Number of MC cycles: 1
Number of molecules: 180
Temperature [K]: 298.00000
External pressure [kPa]: 101.32500
Initial Energies for Box 1
Total molecules in this box 180
Molecules of type 1 : 180
total vibration 103648.308 [K] 205.97156 [kcal/mol]
regular 103648.308 [K] 205.97156 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 86364.564 [K] 171.62503 [kcal/mol]
regular 86364.564 [K] 171.62503 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 51433.187 [K] 102.20884 [kcal/mol]
regular 51433.187 [K] 102.20884 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -630878.399 [K] -1253.69155 [kcal/mol]
intramolecular -11106.088 [K] -22.07019 [kcal/mol]
2-body nonbond -619772.310 [K] -1231.62135 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic 0.000 [K] 0.00000 [kcal/mol]
real space 0.000 [K] 0.00000 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 0.000 [K] 0.00000 [kcal/mol]
self 0.000 [K] 0.00000 [kcal/mol]
correction 0.000 [K] 0.00000 [kcal/mol]
recip sum 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 -389432.3389 [K] -773.886114 [kcal/mol]
initial virial pressure in box 1 = 683.05
+++++ 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) 32.21930 0.00000 0.00000
hmatrix(2,x) 0.00000 32.21930 0.00000
hmatrix(3,x) 0.00000 0.00000 32.21930
* 3D Volume Change Moves *
Box 1 Tries: 4 Acp. Ratio: 0.500 Max Disp.: 0.601E+03
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 8 8 5 100.00 62.50
2 17 17 10 100.00 58.82
3 6 6 3 100.00 50.00
4 25 25 0 100.00 0.00
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 63. Accepted: 29. Accepted: 46.032 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 57. Accepted: 17. Accepted: 29.825 %
Final Energies for Box 1
Total molecules in this box 180
Molecules of type 1 : 180
total vibration 107185.608 [K] 213.00094 [kcal/mol]
regular 107185.608 [K] 213.00094 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 87150.901 [K] 173.18765 [kcal/mol]
regular 87150.901 [K] 173.18765 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 48106.433 [K] 95.59787 [kcal/mol]
regular 48106.433 [K] 95.59787 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -630674.401 [K] -1253.28616 [kcal/mol]
intramolecular -11230.249 [K] -22.31693 [kcal/mol]
2-body nonbond -619444.152 [K] -1230.96923 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic 0.000 [K] 0.00000 [kcal/mol]
real space 0.000 [K] 0.00000 [kcal/mol]
intramolec. 0.000 [K] 0.00000 [kcal/mol]
intermolec. 0.000 [K] 0.00000 [kcal/mol]
self 0.000 [K] 0.00000 [kcal/mol]
correction 0.000 [K] 0.00000 [kcal/mol]
recip sum 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 -388231.4595 [K] -771.499707 [kcal/mol]
Averages Units Type Box 1
Volume nm^3 0.33335E+02
Volume^2 nm^6 0.11112E+04
Molecule Number 1 180.000
Molar Volume ml/mol 0.11152E+03
Specific Density g/ml 0.80870215
Number Density nm-3 1 5.39982
Mole Fraction 1 1.0000000
Radius of Gyration A 1 1.8082136
Ideal Pressure kPa 0.22223E+05
Ideal p_i <N/V>kT kPa 1 0.22223E+05
-<dU/dV> kPa -.30732E+03
Thermodynamic Pressure kPa 0.21916E+05
Thermo p_i <x_1><p_t> kPa 1 0.21916E+05
Total Classical K -0.3886E+06
Inter vdw K -0.6190E+06
Angle K 0.8603E+05
Torsion K 0.5000E+05
Intra vdw K -0.1116E+05
External Field K 0.0000E+00
Vibration K 0.1055E+06
Coulomb K 0.0000E+00
Tail vdw K 0.0000E+00
Solvation K 0.0000E+00
G: Sum{<u_i><N_i>} kJ/mol 0.0000E+00
U kJ/mol -0.3231E+04
Please see towhee_citations for a list of suggested citations for this simulation
