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/Isobaric_Isothermal_Ensemble/Dick1994_PETN/
inputformat: Towhee
ensemble: npt
temperature: 300.000
pressure: 100.000
nmolty: 1
nmolectyp: 72
numboxes: 1
stepstyle: cycles
nstep: 0
printfreq: 1
blocksize: 20
moviefreq: 1000
backupfreq: 10000
runoutput: none
No output of updates or block averages
pdb_output_freq: 1
loutlammps: T
trmaxdispfreq: 10
volmaxdispfreq: 10
potentialstyle: internal
ffnumber: 2
ff_filename:
/towheebase/ForceFields/towhee_ff_Weiner1986
/towheebase/ForceFields/towhee_ff_Dick1994
classical_potential: 12-6 plus 12-10 H-bond
READCLASSICAL: pot_num: 5 potential name: 12-6 plus 12-10 H-bond
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: F
rmin: 0.00000
rcut: 10.0000
rcutin: 5.00000
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
opening forcefield file: 2
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: T
initboxtype: unit cell
Box: 1 inix,iniy,iniz: 3 3 4
pmvol: 0.00000
pmvlpr: 1.00000
rmvol: 0.100000
tavol: 0.500000
pmcell: 0.00000
pmcellpr: 1.00000
rmcell: 1.00000
tacell: 0.500000
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000
pmavb1: 0.00000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 3.00000
pmavb2: 0.00000
pmavb2in: 0.500000
pmavb2mt: 1.00000
moltyp: 1 pmavb2ct: 1.000000
avb2rad: 3.00000
pmavb3: 0.00000
pmavb3mt: 1.00000
moltyp: 1 pmavb3ct: 1.000000
avb3rad: 3.00000
pmcb: 0.00000
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: 1.00000
planewidth: 3.00000
pmrow: 0.00000
pmrowbox: 1.00000
rowwidth: 3.00000
pmtraat: 0.00000
pmtamt: 1.00000
rmtraa: 0.500000
tatraa: 0.500000
pmtracm: 0.00000
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: 29
nmaxcbmc: 29
lpdbnames: F
using the Weiner1986 force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:CT charge: -0.47600
unit: 2 name:CT charge: -0.03000
unit: 3 name:OS charge: -0.47600
unit: 4 name:NN charge: 0.77100
unit: 5 name:HC charge: 0.29400
unit: 6 name:HC charge: 0.29400
unit: 7 name:O charge: -0.36700
unit: 8 name:O charge: -0.36700
unit: 9 name:CT charge: -0.03000
unit: 10 name:OS charge: -0.47600
unit: 11 name:NN charge: 0.77100
unit: 12 name:HC charge: 0.29400
unit: 13 name:HC charge: 0.29400
unit: 14 name:O charge: -0.36700
unit: 15 name:O charge: -0.36700
unit: 16 name:CT charge: -0.03000
unit: 17 name:OS charge: -0.47600
unit: 18 name:NN charge: 0.77100
unit: 19 name:HC charge: 0.29400
unit: 20 name:HC charge: 0.29400
unit: 21 name:O charge: -0.36700
unit: 22 name:O charge: -0.36700
unit: 23 name:CT charge: -0.03000
unit: 24 name:OS charge: -0.47600
unit: 25 name:NN charge: 0.77100
unit: 26 name:HC charge: 0.29400
unit: 27 name:HC charge: 0.29400
unit: 28 name:O charge: -0.36700
unit: 29 name:O charge: -0.36700
Verifying input structures are consistent
Determining CBMC bond distributions
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: 47 Style: Standard Harmonic Length: 1.5260 Constant: 155997.1
Type: 48 Style: Standard Harmonic Length: 1.0900 Constant: 166564.7
Type: 59 Style: Standard Harmonic Length: 1.4100 Constant: 161029.3
Type: 60 Style: Standard Harmonic Length: 1.1955 Constant: 226447.5
Type: 61 Style: Standard Harmonic Length: 1.4026 Constant: 150965.0
Angle Types
Type: 33 Style: Standard Harmonic Angle: 109.500 Constant: 17612.6
Type: 118 Style: Standard Harmonic Angle: 109.500 Constant: 20128.7
Type: 119 Style: Standard Harmonic Angle: 109.500 Constant: 25160.8
Type: 128 Style: Standard Harmonic Angle: 115.000 Constant: 35225.2
Type: 129 Style: Standard Harmonic Angle: 130.330 Constant: 35225.2
Type: 130 Style: Standard Harmonic Angle: 113.200 Constant: 35225.2
Torsion Types
Type: 79 Style: Amber Cosine Series / Total Torsions n: 1
Index 1 k: 654.2 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (0.500) 1-4 coulomb
Type: 85 Style: Amber Cosine Series / Total Torsions n: 1
Index 1 k: 578.7 m:3.0 d: 0.0000000
with 1-4 vdw and scaled (0.500) 1-4 coulomb
Type: 146 Style: Amber Cosine Series / Total Torsions n: 1
Index 1 k: 452.9 m:2.0 d: 3.1415927
with 1-4 vdw and scaled (0.500) 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 316.1342 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
cell_initmol: 2
cell_hmatrix: 9.37986 0.00000 0.00000
cell_hmatrix: 0.00000 9.37986 0.00000
cell_hmatrix: 0.00000 0.00000 6.70876
Box idim hinverse: 1 1 0.03554 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.03554 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.03726
Box: 1 Initial calp: 0.20868
Box: 1 Initial kmax: 5
Finished initconf
initial readtowhee
ibox,testchain,nunit 1 1 29
xold,yold,zold 0.178004E-01 -.127025E-05 -.910384E-06
dx,dy,dz 0.00000 28.1396 26.8350
initial readtowhee
ibox,testchain,nunit 1 3 29
xold,yold,zold 0.178004E-01 9.37986 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 5 29
xold,yold,zold 0.178004E-01 18.7597 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 7 29
xold,yold,zold 9.39766 -.127025E-05 -.910384E-06
dx,dy,dz 0.00000 28.1396 26.8350
initial readtowhee
ibox,testchain,nunit 1 9 29
xold,yold,zold 9.39766 9.37986 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 11 29
xold,yold,zold 9.39766 18.7597 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 13 29
xold,yold,zold 18.7775 -.127025E-05 -.910384E-06
dx,dy,dz 0.00000 28.1396 26.8350
initial readtowhee
ibox,testchain,nunit 1 15 29
xold,yold,zold 18.7775 9.37986 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 17 29
xold,yold,zold 18.7775 18.7597 -.910384E-06
dx,dy,dz 0.00000 0.00000 26.8350
initial readtowhee
ibox,testchain,nunit 1 19 29
xold,yold,zold 0.178004E-01 -.127025E-05 6.70875
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 25 29
xold,yold,zold 9.39766 -.127025E-05 6.70875
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 31 29
xold,yold,zold 18.7775 -.127025E-05 6.70875
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 37 29
xold,yold,zold 0.178004E-01 -.127025E-05 13.4175
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 43 29
xold,yold,zold 9.39766 -.127025E-05 13.4175
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 49 29
xold,yold,zold 18.7775 -.127025E-05 13.4175
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 55 29
xold,yold,zold 0.178004E-01 -.127025E-05 20.1263
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 61 29
xold,yold,zold 9.39766 -.127025E-05 20.1263
dx,dy,dz 0.00000 28.1396 0.00000
initial readtowhee
ibox,testchain,nunit 1 67 29
xold,yold,zold 18.7775 -.127025E-05 20.1263
dx,dy,dz 0.00000 28.1396 0.00000
Energies exclusively from internal potentials
Nonbonded Force Field
12-6 LJ plus 12-10 Hydrogen bond potential
u(r) = 4*epsilon[(sigma/r)^12 - (sigma/r)^6] + C/(r^12) - D/(r^10) - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4 sig 1-4 eps C D 1-4 C 1-4 D
21 CT 21 CT 3.207 30.193 0.000 3.207 15.096 0.000E+00 0.000E+00 0.000E+00 0.000E+00
21 CT 27 HC 2.976 12.326 0.000 2.976 6.163 0.000E+00 0.000E+00 0.000E+00 0.000E+00
21 CT 40 O 3.029 55.125 0.000 3.029 27.562 0.000E+00 0.000E+00 0.000E+00 0.000E+00
21 CT 43 OS 3.074 47.739 0.000 3.074 23.870 0.000E+00 0.000E+00 0.000E+00 0.000E+00
21 CT 47 NN 3.029 55.125 0.000 3.029 27.562 0.000E+00 0.000E+00 0.000E+00 0.000E+00
27 HC 27 HC 2.744 5.032 0.000 2.744 2.516 0.000E+00 0.000E+00 0.000E+00 0.000E+00
27 HC 40 O 2.797 22.505 0.000 2.797 11.252 0.000E+00 0.000E+00 0.000E+00 0.000E+00
27 HC 43 OS 2.842 19.489 0.000 2.842 9.745 0.000E+00 0.000E+00 0.000E+00 0.000E+00
27 HC 47 NN 2.797 22.505 0.000 2.797 11.252 0.000E+00 0.000E+00 0.000E+00 0.000E+00
40 O 40 O 2.851 100.643 0.000 2.851 50.322 0.000E+00 0.000E+00 0.000E+00 0.000E+00
40 O 43 OS 2.895 87.160 0.000 2.895 43.580 0.000E+00 0.000E+00 0.000E+00 0.000E+00
40 O 47 NN 2.851 100.643 0.000 2.851 50.322 0.000E+00 0.000E+00 0.000E+00 0.000E+00
43 OS 43 OS 2.940 75.482 0.000 2.940 37.741 0.000E+00 0.000E+00 0.000E+00 0.000E+00
43 OS 47 NN 2.895 87.160 0.000 2.895 43.580 0.000E+00 0.000E+00 0.000E+00 0.000E+00
47 NN 47 NN 2.851 100.643 0.000 2.851 50.322 0.000E+00 0.000E+00 0.000E+00 0.000E+00
Number of MC cycles: 0
Number of molecules: 72
Temperature [K]: 300.00000
External pressure [kPa]: 100.00000
Initial Energies for Box 1
Total molecules in this box 72
Molecules of type 1 : 72
total vibration 488579.290 [K] 970.91250 [kcal/mol]
regular 488579.290 [K] 970.91250 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 182065.859 [K] 361.80416 [kcal/mol]
regular 182065.859 [K] 361.80416 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 2111015.914 [K] 4195.04427 [kcal/mol]
regular 2111015.914 [K] 4195.04427 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -895843.958 [K] -1780.23531 [kcal/mol]
intramolecular 96561.696 [K] 191.88893 [kcal/mol]
2-body nonbond -992405.654 [K] -1972.12424 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic -3513769.869 [K] -6982.61915 [kcal/mol]
real space -2671818.529 [K] -5309.48011 [kcal/mol]
intramolec. -1889048.711 [K] -3753.94753 [kcal/mol]
intermolec. -782769.819 [K] -1555.53259 [kcal/mol]
self -7483771.942 [K] -14871.87017 [kcal/mol]
correction 6641010.858 [K] 13197.12199 [kcal/mol]
recip sum 809.744 [K] 1.60914 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1627952.7646 [K] -3235.093526 [kcal/mol]
+++++ 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) 28.13958 0.00000 0.00000
hmatrix(2,x) 0.00000 28.13958 0.00000
hmatrix(3,x) 0.00000 0.00000 26.83502
Final Energies for Box 1
Total molecules in this box 72
Molecules of type 1 : 72
total vibration 488579.290 [K] 970.91250 [kcal/mol]
regular 488579.290 [K] 970.91250 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 182065.859 [K] 361.80416 [kcal/mol]
regular 182065.859 [K] 361.80416 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 2111015.914 [K] 4195.04427 [kcal/mol]
regular 2111015.914 [K] 4195.04427 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -895843.958 [K] -1780.23531 [kcal/mol]
intramolecular 96561.696 [K] 191.88893 [kcal/mol]
2-body nonbond -992405.654 [K] -1972.12424 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic -3513769.869 [K] -6982.61915 [kcal/mol]
real space -2671818.529 [K] -5309.48011 [kcal/mol]
intramolec. -1889048.711 [K] -3753.94753 [kcal/mol]
intermolec. -782769.819 [K] -1555.53259 [kcal/mol]
self -7483771.942 [K] -14871.87017 [kcal/mol]
correction 6641010.858 [K] 13197.12199 [kcal/mol]
recip sum 809.744 [K] 1.60914 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -1627952.7646 [K] -3235.093526 [kcal/mol]
Please see towhee_citations for a list of suggested citations for this simulation
