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
random_number_generator: DX-1597-2-7
random_allow_restart: T
ensemble: nvt
temperature: 480.000
nmolty: 1
nmolectyp: 64
numboxes: 1
stepstyle: cycles
nstep: 0
printfreq: 100
blocksize: 200
moviefreq: 100
backupfreq: 100
restartfreq: 0
runoutput: full
Full output of updates and block averages
pdb_output_freq: 0
loutdft: F
loutlammps: T
loutdlpoly: F
pressurefreq: 10
trmaxdispfreq: 100
volmaxdispfreq: 100
chempotperstep: 0
potentialstyle: internal
ffnumber: 1
ff_filename:
towhee_ff
classical_potential: Lennard-Jones
READCLASSICAL: pot_num: 1 potential name: Lennard-Jones
classical_mixrule: Lorentz-Berthelot
lshift: F
ltailc: F
rmin: 0.00000
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
max_bond_length: 3.00000
nfield: 0
solvation_style: none
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
coords
Box: 1 initlattice: none
Box: 1 initmol: 64
Box: 1 inix,iniy,iniz: 4 4 4
Box idim hmatrix: 1 1 29.10100 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 29.10100 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 29.10100
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000
pmavb1: 0.00000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 0.100000
pmavb2: 0.00000
pmavb2in: 0.500000
pmavb2mt: 1.00000
moltyp: 1 pmavb2ct: 1.000000
avb2rad: 0.100000
pmavb3: 0.00000
pmavb3mt: 1.00000
moltyp: 1 pmavb3ct: 1.000000
avb3rad: 0.100000
pmcb: 0.00000
pmcbmt: 1.00000
pmall: 0.00000
pmback: 0.00000
pmbkmt: 1.00000
pmcbside: 0.00000
pmcbsidemt: 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: 1.00000
pmrow: 0.00000
pmrowbox: 1.00000
rowwidth: 1.00000
pmtraat: 0.00000
pmtamt: 1.00000
rmtraa: 0.500000
tatraa: 0.500000
pmcomposite: 0.00000
pmcomt: 1.00000
rmcomtra: 0.500000
rmcomrot: 0.500000
pmtracm: 0.00000
pmtcmt: 1.00000
rmtrac: 0.500000
tatrac: 0.500000
pmrotate: 1.00000
pmromt: 1.00000
rmrot: 0.500000
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: 10
nmaxcbmc: 10
bead: 1 beadtype: 1 charge: 0.00000
bead: 2 beadtype: 2 charge: 0.00000
bead: 3 beadtype: 2 charge: 0.00000
bead: 4 beadtype: 2 charge: 0.00000
bead: 5 beadtype: 2 charge: 0.00000
bead: 6 beadtype: 2 charge: 0.00000
bead: 7 beadtype: 2 charge: 0.00000
bead: 8 beadtype: 2 charge: 0.00000
bead: 9 beadtype: 2 charge: 0.00000
bead: 10 beadtype: 3 charge: 0.00000
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: 1 Style: Standard Harmonic Length: 1.5400 Constant: 226271.3
Angle Types
Type: 1 Style: Standard Harmonic Angle: 114.000 Constant: 31225.6
Torsion Types
Type: 1 Style: Cosine Power Series Sum x=1,Ntor a(x) Cos(phi)^x
Ntor: 4
a(0): 1009.86
a(1): -2018.71
a(2): 136.365
a(3): 3164.94
a(4): 0.00000
Improper Torsion Types
No Improper Types
Canonical 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 142.2838 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
Box idim hinverse: 1 1 0.03436 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.03436 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.03436
Box: 1 Initial calp: 0.19243
Box: 1 Initial kmax: 5
Finished initconf
initial readtowhee
ibox,testchain,nunit 1 1 10
xold,yold,zold 0.132216 29.3504 11.0706
dx,dy,dz 0.00000 -29.1010 0.00000
initial readtowhee
ibox,testchain,nunit 1 13 10
xold,yold,zold 29.3382 16.0022 6.86291
dx,dy,dz -29.1010 0.00000 0.00000
initial readtowhee
ibox,testchain,nunit 1 23 10
xold,yold,zold 24.8065 11.2053 29.1114
dx,dy,dz 0.00000 0.00000 -29.1010
initial readtowhee
ibox,testchain,nunit 1 40 10
xold,yold,zold 23.9877 18.1363 29.6430
dx,dy,dz 0.00000 0.00000 -29.1010
initial readtowhee
ibox,testchain,nunit 1 52 10
xold,yold,zold 29.1184 16.3924 26.8680
dx,dy,dz -29.1010 0.00000 0.00000
Energies exclusively from internal potentials
Nonbonded Force Field
Lennard-Jones 12-6 potential
u(r) = 4*epsilon[(sigma/r)^12 - (sigma/r)^6] - shift
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4sig 1-4eps
1 no name 1 no name 3.9300 114.2302 0.0000 3.9300 114.2302
1 no name 2 no name 3.9300 73.1155 0.0000 3.9300 73.1155
1 no name 3 no name 3.9300 114.2302 0.0000 3.9300 114.2302
2 no name 2 no name 3.9300 46.7991 0.0000 3.9300 46.7991
2 no name 3 no name 3.9300 73.1155 0.0000 3.9300 73.1155
3 no name 3 no name 3.9300 114.2302 0.0000 3.9300 114.2302
Number of MC cycles: 0
Number of molecules: 64
Temperature [K]: 480.00000
Initial Energies for Box 1
Total molecules in this box 64
Molecules of type 1 : 64
total vibration 15712.521 [K] 31.22417 [kcal/mol]
regular 15712.521 [K] 31.22417 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 56002.429 [K] 111.28891 [kcal/mol]
regular 56002.429 [K] 111.28891 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 245683.333 [K] 488.22581 [kcal/mol]
regular 245683.333 [K] 488.22581 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 85713.768 [K] 170.33176 [kcal/mol]
intramolecular 50765.282 [K] 100.88157 [kcal/mol]
2-body nonbond 34948.486 [K] 69.45019 [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 403112.0505 [K] 801.070653 [kcal/mol]
initial virial pressure in box 1 = 1649141.89
+++++ 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) 29.10100 0.00000 0.00000
hmatrix(2,x) 0.00000 29.10100 0.00000
hmatrix(3,x) 0.00000 0.00000 29.10100
Final Energies for Box 1
Total molecules in this box 64
Molecules of type 1 : 64
total vibration 15712.521 [K] 31.22417 [kcal/mol]
regular 15712.521 [K] 31.22417 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 56002.429 [K] 111.28891 [kcal/mol]
regular 56002.429 [K] 111.28891 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion 245683.333 [K] 488.22581 [kcal/mol]
regular 245683.333 [K] 488.22581 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 85713.768 [K] 170.33176 [kcal/mol]
intramolecular 50765.282 [K] 100.88157 [kcal/mol]
2-body nonbond 34948.486 [K] 69.45019 [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 403112.0505 [K] 801.070653 [kcal/mol]
Please see towhee_citations for a list of suggested citations for this simulation
