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: 410.000
nmolty: 1
nmolectyp: 120
numboxes: 2
stepstyle: cycles
nstep: 1
printfreq: 1
blocksize: 2
moviefreq: 100000
backupfreq: 1000
runoutput: full
Full output of updates and block averages
pdb_output_freq: 0
pressurefreq: 20
trmaxdispfreq: 1000
volmaxdispfreq: 1000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_Amber96
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
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
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: 80
Box: 2 initmol: 40
Box: 1 inix,iniy,iniz: 5 5 5
Box: 2 inix,iniy,iniz: 4 4 4
Box idim hmatrix: 1 1 22.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 22.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 22.00000
Box idim hmatrix: 2 1 200.00000 0.00000 0.00000
Box idim hmatrix: 2 2 0.00000 200.00000 0.00000
Box idim hmatrix: 2 3 0.00000 0.00000 200.00000
itest: 1 pairbox: 1 2
pmvol: 0.200000E-02
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pm2boxcbswap: 0.200000
pm2cbswmt: 1.00000
pm2cbswpr: 1.00000
pmcb: 0.400000
pmcbmt: 1.00000
pmall: 0.00000
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 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: 12
nmaxcbmc: 12
lpdbnames: F
using the Amber96 force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:CT charge: -0.24380
unit: 2 name:CT charge: 0.36400
unit: 3 name:CT charge: -0.24380
unit: 4 name:OH charge: -0.67610
unit: 5 name:HO charge: 0.41020
unit: 6 name:HC charge: 0.06420
unit: 7 name:HC charge: 0.06420
unit: 8 name:HC charge: 0.06420
unit: 9 name:H1 charge: 0.00430
unit: 10 name:HC charge: 0.06420
unit: 11 name:HC charge: 0.06420
unit: 12 name:HC charge: 0.06420
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: 40 Style: Standard Harmonic Length: 1.5260 Constant: 155997.1
Type: 42 Style: Standard Harmonic Length: 1.0900 Constant: 171093.6
Type: 47 Style: Standard Harmonic Length: 1.4100 Constant: 161029.3
Type: 51 Style: Standard Harmonic Length: 0.9600 Constant: 278278.8
Angle Types
Type: 9 Style: Standard Harmonic Angle: 109.500 Constant: 25160.8
Type: 69 Style: Standard Harmonic Angle: 109.500 Constant: 20128.7
Type: 77 Style: Standard Harmonic Angle: 108.500 Constant: 27676.9
Type: 84 Style: Standard Harmonic Angle: 109.500 Constant: 17612.6
Torsion Types
Type: 23 Style: Amber/Charmm/Gromos Cosine Series n: 1
Index 1 k: 78.3 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (0.833) 1-4 coulomb
Type: 24 Style: Amber/Charmm/Gromos Cosine Series n: 1
Index 1 k: 83.9 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (0.833) 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
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 60.0959 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: 0.513519
Max displacement for COM translate: 0.545930
Max displacement for rotation: 0.393696
box: 2
molecule type: 1
Max displacement for Atom translate: 20.000000
Max displacement for COM translate: 20.000000
Max displacement for rotation: 3.141500
Max disp. for 3D Volume: 0.2751E-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): 24.63894 0.00000 0.00000
Box 1 hmatrix(2,x): 0.00000 24.63894 0.00000
Box 1 hmatrix(3,x): 0.00000 0.00000 24.63894
Box 2 hmatrix(1,x): 59.74048 0.00000 0.00000
Box 2 hmatrix(2,x): 0.00000 59.74048 0.00000
Box 2 hmatrix(3,x): 0.00000 0.00000 59.74048
Box: 1 Initial calp: 0.22728
Box: 1 Initial kmax: 5
Box: 2 Initial calp: 0.09374
Box: 2 Initial kmax: 5
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
13 CT 13 CT 3.3997 55.0519 0.0000 3.3997 27.5259
13 CT 17 H1 2.9355 20.8552 0.0000 2.9355 10.4276
13 CT 23 HC 3.0246 20.8552 0.0000 3.0246 10.4276
13 CT 24 HO 1.6998 0.0000 0.0000 1.6998 0.0000
13 CT 40 OH 3.2331 76.3460 0.0000 3.2331 38.1730
17 H1 17 H1 2.4714 7.9005 0.0000 2.4714 3.9503
17 H1 23 HC 2.5604 7.9005 0.0000 2.5604 3.9503
17 H1 24 HO 1.2357 0.0000 0.0000 1.2357 0.0000
17 H1 40 OH 2.7689 28.9220 0.0000 2.7689 14.4610
23 HC 23 HC 2.6495 7.9005 0.0000 2.6495 3.9503
23 HC 24 HO 1.3248 0.0000 0.0000 1.3248 0.0000
23 HC 40 OH 2.8580 28.9220 0.0000 2.8580 14.4610
24 HO 24 HO 0.0000 0.0000 0.0000 0.0000 0.0000
24 HO 40 OH 1.5332 0.0000 0.0000 1.5332 0.0000
40 OH 40 OH 3.0665 105.8768 0.0000 3.0665 52.9384
Number of MC cycles: 1
Number of molecules: 120
Temperature [K]: 410.00000
Initial Energies for Box 1
Total molecules in this box 98
Molecules of type 1 : 98
total vibration 221044.557 [K] 439.26325 [kcal/mol]
regular 221044.557 [K] 439.26325 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 311182.904 [K] 618.38760 [kcal/mol]
regular 311182.904 [K] 618.38760 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -2568727.445 [K] -5104.61588 [kcal/mol]
regular -2568727.445 [K] -5104.61588 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -197904.842 [K] -393.27964 [kcal/mol]
intramolecular 3452.624 [K] 6.86111 [kcal/mol]
2-body nonbond -188596.759 [K] -374.78247 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -12760.707 [K] -25.35828 [kcal/mol]
total coulombic 863161.921 [K] 1715.28904 [kcal/mol]
real space 176265.612 [K] 350.27782 [kcal/mol]
intramolec. 337698.677 [K] 671.08016 [kcal/mol]
intermolec. -161433.064 [K] -320.80234 [kcal/mol]
self -1893029.575 [K] -3761.85836 [kcal/mol]
correction 2569966.560 [K] 5107.07826 [kcal/mol]
recip sum 9959.323 [K] 19.79132 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1371242.9050 [K] -2724.955625 [kcal/mol]
Initial Energies for Box 2
Total molecules in this box 22
Molecules of type 1 : 22
total vibration 56144.118 [K] 111.57048 [kcal/mol]
regular 56144.118 [K] 111.57048 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 67972.696 [K] 135.07642 [kcal/mol]
regular 67972.696 [K] 135.07642 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -577236.535 [K] -1147.09359 [kcal/mol]
regular -577236.535 [K] -1147.09359 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -169.886 [K] -0.33760 [kcal/mol]
intramolecular 608.818 [K] 1.20985 [kcal/mol]
2-body nonbond -733.589 [K] -1.45780 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -45.116 [K] -0.08965 [kcal/mol]
total coulombic 233688.542 [K] 464.38957 [kcal/mol]
real space 160086.933 [K] 318.12729 [kcal/mol]
intramolec. 162154.553 [K] 322.23610 [kcal/mol]
intermolec. -2067.620 [K] -4.10881 [kcal/mol]
self -175269.902 [K] -348.29913 [kcal/mol]
correction 248657.781 [K] 494.13668 [kcal/mol]
recip sum 213.730 [K] 0.42473 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -219601.0659 [K] -436.394717 [kcal/mol]
initial virial pressure in box 1 = -25854.93
initial virial pressure in box 2 = 349.83
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 -0.1384E+07 0.1496E+05 -25854.9 99
B: 2 -0.2019E+06 0.2132E+06 349.8 21
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 24.63894 0.00000 0.00000
hmatrix(2,x) 0.00000 24.63894 0.00000
hmatrix(3,x) 0.00000 0.00000 24.63894
Box: 2
hmatrix(1,x) 59.74048 0.00000 0.00000
hmatrix(2,x) 0.00000 59.74048 0.00000
hmatrix(3,x) 0.00000 0.00000 59.74048
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 2 to box 1 Attempted: 17 Grown: 17 Accepted: 1
From box 1 to box 2 Attempted: 10 Grown: 10 Accepted: 0
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 1 1 1 100.00 100.00
10 3 3 0 100.00 0.00
11 15 15 0 100.00 0.00
Molecule type: 1 Box: 2
Length Attempts Regrown Accepted %Regrown %Accep.
1 1 1 1 100.00 100.00
7 1 1 1 100.00 100.00
10 2 2 1 100.00 50.00
11 1 1 0 100.00 0.00
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 31. Accepted: 17. Accepted: 54.839 %
Molecule: 1 Box: 2 Attempts: 3. Accepted: 2. Accepted: 66.667 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 27. Accepted: 9. Accepted: 33.333 %
Molecule: 1 Box: 2 Attempts: 8. Accepted: 7. Accepted: 87.500 %
Final Energies for Box 1
Total molecules in this box 99
Molecules of type 1 : 99
total vibration 223637.024 [K] 444.41504 [kcal/mol]
regular 223637.024 [K] 444.41504 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 312925.252 [K] 621.85002 [kcal/mol]
regular 312925.252 [K] 621.85002 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -2595206.846 [K] -5157.23616 [kcal/mol]
regular -2595206.846 [K] -5157.23616 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -196601.752 [K] -390.69012 [kcal/mol]
intramolecular 3457.687 [K] 6.87117 [kcal/mol]
2-body nonbond -187036.982 [K] -371.68285 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -13022.458 [K] -25.87843 [kcal/mol]
total coulombic 871219.249 [K] 1731.30070 [kcal/mol]
real space 177158.285 [K] 352.05175 [kcal/mol]
intramolec. 341914.467 [K] 679.45785 [kcal/mol]
intermolec. -164756.183 [K] -327.40610 [kcal/mol]
self -1912346.203 [K] -3800.24467 [kcal/mol]
correction 2596342.974 [K] 5159.49389 [kcal/mol]
recip sum 10064.194 [K] 19.99973 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1384027.0731 [K] -2750.360527 [kcal/mol]
Final Energies for Box 2
Total molecules in this box 21
Molecules of type 1 : 21
total vibration 57691.138 [K] 114.64474 [kcal/mol]
regular 57691.138 [K] 114.64474 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 66495.897 [K] 132.14170 [kcal/mol]
regular 66495.897 [K] 132.14170 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -548682.076 [K] -1090.34971 [kcal/mol]
regular -548682.076 [K] -1090.34971 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -127.968 [K] -0.25430 [kcal/mol]
intramolecular 630.742 [K] 1.25342 [kcal/mol]
2-body nonbond -717.602 [K] -1.42603 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
tail correct. -41.108 [K] -0.08169 [kcal/mol]
total coulombic 222739.550 [K] 442.63156 [kcal/mol]
real space 152507.586 [K] 303.06549 [kcal/mol]
intramolec. 154745.766 [K] 307.51324 [kcal/mol]
intermolec. -2238.180 [K] -4.44775 [kcal/mol]
self -167303.088 [K] -332.46735 [kcal/mol]
correction 237355.436 [K] 471.67648 [kcal/mol]
recip sum 179.615 [K] 0.35693 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -201883.4584 [K] -401.186007 [kcal/mol]
Averages Units Type Box 1 Box 2
Volume nm^3 0.14958E+02 0.21321E+03
Volume^2 nm^6 0.22373E+03 0.45458E+05
Molecule Number 1 98.050 21.950
Molar Volume ml/mol 0.91868E+02 0.58495E+04
Specific Density g/ml 0.65415757 0.01027376
Number Density nm-3 1 6.55513 0.10295
Mole Fraction 1 1.0000000 1.0000000
Radius of Gyration A 1 1.3610946 1.3631387
Ideal Pressure kPa 0.37118E+05 0.58294E+03
Ideal p_i <N/V>kT kPa 1 0.37118E+05 0.58294E+03
Total Classical K -0.1371E+07 -0.2143E+06
Inter vdw K -0.1997E+06 -0.7457E+03
Angle K 0.3114E+06 0.6767E+05
Torsion K -0.2570E+07 -0.5745E+06
Intra vdw K 0.3453E+04 0.6545E+03
External Field K 0.0000E+00 0.0000E+00
Vibration K 0.2213E+06 0.5978E+05
Coulomb K 0.8623E+06 0.2329E+06
Tail vdw K -0.1277E+05 -0.4492E+02
Solvation K 0.0000E+00 0.0000E+00
u (Density) K 1 -4762.667 -6465.707
u (NVT Insertion) K 1 20953.850 21567.302
u (NpT Insertion) K 1 20953.850 21567.302
u (Den. + NVT Insert) K 1 16191.183 15101.596
u (Den. + NpT Insert) K 1 16191.183 15101.596
u (Gibbs Total) K 1 16195.136 15115.327
G: Sum{<u_i><N_i>} kJ/mol 0.1320E+05 0.2758E+04
U kJ/mol -0.1140E+05 -0.1782E+04
H_vap (pV/n=RT) kJ/mol 0.3853E+02
Please see towhee_citations for a list of suggested citations for this simulation
