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: 10.0000
nmolty: 1
nmolectyp: 10
numboxes: 1
stepstyle: cycles
nstep: 10
printfreq: 1
blocksize: 2
moviefreq: 100000
backupfreq: 1000
runoutput: full
Full output of updates and block averages
pdb_output_freq: 100000
pressurefreq: 1
trmaxdispfreq: 5
volmaxdispfreq: 100000
potentialstyle: internal
ffnumber: 1
ff_filename:
/towheebase/ForceFields/towhee_ff_SquareWell
classical_potential: Square Well
READCLASSICAL: pot_num: 17 potential name: Square Well
classical_mixrule: Lorentz-Berthelot
radial_pressure_delta: 0.100000E-01
electrostatic_form: none
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: T
initboxtype: dimensions
initstyle Box: 1
full cbmc
Box: 1 initlattice: simple cubic
Box: 1 initmol: 10
Box: 1 inix,iniy,iniz: 4 3 3
Box idim hmatrix: 1 1 20.00000 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 20.00000 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 20.00000
pm1boxcbswap: 0.200000
pm1cbswmt: 1.00000
pmavb1: 0.00000
pmavb1in: 0.500000
pmavb1mt: 1.00000
moltyp: 1 pmavb1ct: 1.000000
avb1rad: 0.500000E-01
pmavb2: 0.00000
pmavb2in: 0.500000
pmavb2mt: 1.00000
moltyp: 1 pmavb2ct: 1.000000
avb2rad: 0.500000E-01
pmavb3: 0.00000
pmavb3mt: 1.00000
moltyp: 1 pmavb3ct: 1.000000
avb3rad: 0.500000E-01
pmcb: 0.600000
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: 1.00000
pmrow: 0.00000
pmrowbox: 1.00000
rowwidth: 1.00000
pmtraat: 0.00000
pmtamt: 1.00000
rmtraa: 0.500000
tatraa: 0.500000
pmtracm: 0.900000
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 Siepmann 1999 + Martin and Thompson 2004
Original Coupled-Decoupled formulation from
M.G. Martin; J.I. Siepmann; J. Phys. Chem. B103 2977-2980 (1999)
with a decoupled bond length selection from
M.G. Martin; A.P. Thompson; Fluid Phase Equilib. 217 105-110 (2004)
cbmc_setting_style: Martin and Thompson FPE 2004
input_style: basic connectivity map
nunit: 8
nmaxcbmc: 8
lpdbnames: F
using the SquareWell force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:type_a charge: 0.00000
unit: 2 name:type_a charge: 0.00000
unit: 3 name:type_a charge: 0.00000
unit: 4 name:type_a charge: 0.00000
unit: 5 name:type_a charge: 0.00000
unit: 6 name:type_a charge: 0.00000
unit: 7 name:type_a charge: 0.00000
unit: 8 name:type_a charge: 0.00000
Verifying input structures are consistent
Determining CBMC bond distributions
for molecule type 1
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: Fixed Length: 1.0000
Angle Types
Type: 1 Style: Nonbonded Interaction
Torsion Types
Type: 1 Style: SquareWell Nonbonded terms only
with 1-4 vdw and scaled (1.000) 1-4 coulomb
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
Molecular mass for molecule type 1 is 8.0000 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 0.05000 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.05000 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.05000
INITCONF: building template for molecule type: 1
Initial Structure Growth Trial: 1
Finished initconf
Energies exclusively from internal potentials
Nonbonded Force Field
Square well potential
u(r) = infinity for r < nbcoeff(1)
u(r) = -nbcoeff(3) for nbcoeff(1) < r < nbcoeff(2)
Num. Atom(i) Num. Atom(j) nbcoeff(1) nbcoeff(2) nbcoeff(3)
1 type_a 1 type_a 1.000 1.500 1.000
Number of MC cycles: 10
Number of molecules: 10
Temperature [K]: 10.00000
Initial Energies for Box 1
Total molecules in this box 10
Molecules of type 1 : 10
total vibration 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle -20.000 [K] -0.03974 [kcal/mol]
regular -20.000 [K] -0.03974 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -10.000 [K] -0.01987 [kcal/mol]
regular -10.000 [K] -0.01987 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 0.000 [K] 0.00000 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [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 -30.00000000 [K] -0.0596164753 [kcal/mol]
initial radial pressure in box 1 = 172.63
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] Molecules
1 B: 1 -0.3200E+02 0.8000E+04 172.6 10
2 B: 1 -0.3800E+02 0.8000E+04 172.6 10
Block Averages (BA) for block 1
BA Box: 1 Volume [A^3] 0.80000000E+04
BA Box: 1 V^2 [A^6] 0.64000000E+08
BA Box: 1 Specific density [g/ml] 0.16605655E-01
BA Box: 1 Total Classical -.32900000E+02
BA Box: 1 Inter vdw -.21000000E+01
BA Box: 1 Angle -.22100000E+02
BA Box: 1 Torsion -.82000000E+01
BA Box: 1 Intra vdw -.50000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw 0.00000000E+00
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.12500000E+01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Radius of Gyration Type: 1 1.43096
3 B: 1 -0.3000E+02 0.8000E+04 172.6 10
4 B: 1 -0.3300E+02 0.8000E+04 172.6 10
Block Averages (BA) for block 2
BA Box: 1 Volume [A^3] 0.80000000E+04
BA Box: 1 V^2 [A^6] 0.64000000E+08
BA Box: 1 Specific density [g/ml] 0.16605655E-01
BA Box: 1 Total Classical -.33100000E+02
BA Box: 1 Inter vdw -.31000000E+01
BA Box: 1 Angle -.21800000E+02
BA Box: 1 Torsion -.80000000E+01
BA Box: 1 Intra vdw -.20000000E+00
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw 0.00000000E+00
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.12500000E+01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Radius of Gyration Type: 1 1.41774
Updating maximum translational/rotational displacements
Box: 1 Molecule: 1 Attempts Accepted New Displacement
Translate COM 12. 10. 0.833333
Rotate 3. 3. 0.100000
5 B: 1 -0.4000E+02 0.8000E+04 172.6 10
6 B: 1 -0.3500E+02 0.8000E+04 172.6 10
Block Averages (BA) for block 3
BA Box: 1 Volume [A^3] 0.80000000E+04
BA Box: 1 V^2 [A^6] 0.64000000E+08
BA Box: 1 Specific density [g/ml] 0.16605655E-01
BA Box: 1 Total Classical -.36750000E+02
BA Box: 1 Inter vdw -.10000000E+01
BA Box: 1 Angle -.23450000E+02
BA Box: 1 Torsion -.10700000E+02
BA Box: 1 Intra vdw -.16000000E+01
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw 0.00000000E+00
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.12500000E+01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Radius of Gyration Type: 1 1.40284
7 B: 1 -0.3200E+02 0.8000E+04 172.6 10
8 B: 1 -0.3700E+02 0.8000E+04 172.6 10
Block Averages (BA) for block 4
BA Box: 1 Volume [A^3] 0.80000000E+04
BA Box: 1 V^2 [A^6] 0.64000000E+08
BA Box: 1 Specific density [g/ml] 0.16605655E-01
BA Box: 1 Total Classical -.34350000E+02
BA Box: 1 Inter vdw -.25000000E+00
BA Box: 1 Angle -.23000000E+02
BA Box: 1 Torsion -.96500000E+01
BA Box: 1 Intra vdw -.14500000E+01
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw 0.00000000E+00
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.12500000E+01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Radius of Gyration Type: 1 1.38654
9 B: 1 -0.3700E+02 0.8000E+04 172.6 10
Updating maximum translational/rotational displacements
Box: 1 Molecule: 1 Attempts Accepted New Displacement
Translate COM 16. 16. 1.666667
Rotate 8. 8. 0.200000
10 B: 1 -0.3200E+02 0.8000E+04 172.6 10
Block Averages (BA) for block 5
BA Box: 1 Volume [A^3] 0.80000000E+04
BA Box: 1 V^2 [A^6] 0.64000000E+08
BA Box: 1 Specific density [g/ml] 0.16605655E-01
BA Box: 1 Total Classical -.34050000E+02
BA Box: 1 Inter vdw 0.00000000E+00
BA Box: 1 Angle -.22200000E+02
BA Box: 1 Torsion -.94500000E+01
BA Box: 1 Intra vdw -.24000000E+01
BA Box: 1 External Field 0.00000000E+00
BA Box: 1 Vibration 0.00000000E+00
BA Box: 1 Coulomb 0.00000000E+00
BA Box: 1 Tail vdw 0.00000000E+00
BA Box: 1 Solvation 0.00000000E+00
BA Box: 1 u (Gibbs Total) [K] Type 1 0.00000000E+00
BA Box: 1 Number density [nm-3] Type 1 0.12500000E+01
BA Box: 1 Mol Fraction Type 1 0.10000000E+01
BA Box: 1 Radius of Gyration Type: 1 1.36515
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 20.00000 0.00000 0.00000
hmatrix(2,x) 0.00000 20.00000 0.00000
hmatrix(3,x) 0.00000 0.00000 20.00000
* Configurational-Bias SWAP Moves *
Molecule type: 1
From box 1 to box 1 Attempted: 18 Grown: 18 Accepted: 12
* Configurational-Bias REGROWTH Moves *
Molecule type: 1 Box: 1
Length Attempts Regrown Accepted %Regrown %Accep.
1 3 3 3 100.00 100.00
2 4 4 3 100.00 75.00
3 4 4 1 100.00 25.00
4 13 13 10 100.00 76.92
5 6 6 3 100.00 50.00
6 4 4 2 100.00 50.00
7 9 9 6 100.00 66.67
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 28. Accepted: 26. Accepted: 92.857 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 11. Accepted: 11. Accepted: 100.000 %
Final Energies for Box 1
Total molecules in this box 10
Molecules of type 1 : 10
total vibration 0.000 [K] 0.00000 [kcal/mol]
regular 0.000 [K] 0.00000 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle -20.000 [K] -0.03974 [kcal/mol]
regular -20.000 [K] -0.03974 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -9.000 [K] -0.01788 [kcal/mol]
regular -9.000 [K] -0.01788 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond -3.000 [K] -0.00596 [kcal/mol]
intramolecular -3.000 [K] -0.00596 [kcal/mol]
2-body nonbond 0.000 [K] 0.00000 [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 -32.00000000 [K] -0.0635909070 [kcal/mol]
Averages Units Type Box 1
Volume nm^3 0.80000E+01
Volume^2 nm^6 0.64000E+02
Molecule Number 1 10.000
Molar Volume ml/mol 0.48176E+03
Specific Density g/ml 0.01660565
Number Density nm-3 1 1.25000
Mole Fraction 1 1.0000000
Radius of Gyration A 1 1.4006460
Radial Pressure kPa 0.17263E+03
Radial p_i <x_i><p_v> kPa 1 0.17263E+03
Ideal Pressure kPa 0.17263E+03
Ideal p_i <N/V>kT kPa 1 0.17263E+03
Total Classical K -0.3423E+02
Inter vdw K -0.1290E+01
Angle K -0.2251E+02
Torsion K -0.9200E+01
Intra vdw K -0.1230E+01
External Field K 0.0000E+00
Vibration K 0.0000E+00
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 -0.2846E+00
pV: <p><V> kJ/mol 0.8314E+00
H: <U> + <p><V> kJ/mol 0.5468E+00
H: <U + pV> kJ/mol 0.5437E+00
S: (<H> - <G>)/T kJ/K mol 0.5468E-01
Z: <p><V>/<N>RT 1.000000
C_v: T^2<H^2>-<H>^2 J/K mol 0.1052E+01
Block Averages ( 5 blocks) Units Type Box Average Standard Deviation
Specific Density g/ml 1 0.16606E-01 0.00000E+00
Radial Pressure kPa 1 0.17263E+03 0.00000E+00
Total Classical K 1 -0.34230E+02 0.13743E+01
Inter vdw K 1 -0.12900E+01 0.11629E+01
Angle K 1 -0.22510E+02 0.61514E+00
Torsion K 1 -0.92000E+01 0.99549E+00
Intra vdw K 1 -0.12300E+01 0.79347E+00
External Field K 1 0.00000E+00 0.00000E+00
Vibration K 1 0.00000E+00 0.00000E+00
Coulomb K 1 0.00000E+00 0.00000E+00
Tail vdw K 1 0.00000E+00 0.00000E+00
Solvation K 1 0.00000E+00 0.00000E+00
Number Density nm-3 1 1 0.12500E+01 0.00000E+00
Mole Fraction 1 1 1.0000000 0.0000000
Molarity M 1 1 0.20764E+01 0.00000E+00
Radius of Gyration A 1 1 1.40065 0.02313
-----block averages ------
Box: 1
Block Energy Density Radial Press. Mol fracs
1 -.32900000E+02 0.16605655E-01 0.17263289E+03 1.00000000
2 -.33100000E+02 0.16605655E-01 0.17263289E+03 1.00000000
3 -.36750000E+02 0.16605655E-01 0.17263289E+03 1.00000000
4 -.34350000E+02 0.16605655E-01 0.17263289E+03 1.00000000
5 -.34050000E+02 0.16605655E-01 0.17263289E+03 1.00000000
Please see towhee_citations for a list of suggested citations for this simulation
