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/Canonical_Ensemble/Formamide_Scaled/
inputformat: Towhee
ensemble: nvt
temperature: 298.000
nmolty: 2
nmolectyp: 216 1
numboxes: 1
stepstyle: cycles
nstep: 1
printfreq: 1
blocksize: 25000
moviefreq: 100000000
backupfreq: 100000000
runoutput: full
Full output of updates and block averages
pressurefreq: 100000
trmaxdispfreq: 1000000
volmaxdispfreq: 1000000
potentialstyle: internal
ffnumber: 2
ff_filename:
/towheebase/ForceFields/towhee_ff_TIP4P
/towheebase/ForceFields/towhee_ff_OPLS-aa
classical_potential: Scaled Lennard-Jones
READCLASSICAL: pot_num: 4 potential name: Scaled Lennard-Jones
classical_mixrule: Geometric
cmix_rescaling_style: soft-core
cmix_lambda_lj: 0.500000
cmix_lambda_c: 0.500000
cmix_alpha_lj: 0.500000
cmix_lprintdudl: T
cmix_npair: 5
pair: 1 cmix_pair_list: OPLS-aa C n
pair: 2 cmix_pair_list: OPLS-aa HC~3
pair: 3 cmix_pair_list: OPLS-aa O
pair: 4 cmix_pair_list: OPLS-aa N
pair: 5 cmix_pair_list: OPLS-aa H
num_foreign_lambda: 5
foreign_lambda:
1.00000 1.00000
0.501000 0.499000
0.500000 0.500000
0.499000 0.501000
0.00000 0.00000
lshift: F
rmin: 1.00000
rcut: 9.00000
rcutin: 9.00000
electrostatic_form: coulomb
coulombstyle: minimum image
dielect: 1.00000
Setting up force field parameters from files
opening forcefield file: 1
opening forcefield file: 2
Geometric Mixing rules
Geometric mean of all nonbond coefficients
default max_bond_length: 3.00
No solvation model used
linit: T
initboxtype: dimensions
initstyle Box: 1
coords coords
Box: 1 initlattice: none none
Box: 1 initmol: 216 1
Box: 1 inix,iniy,iniz: 6 6 7
Box idim hmatrix: 1 1 18.68200 0.00000 0.00000
Box idim hmatrix: 1 2 0.00000 18.68200 0.00000
Box idim hmatrix: 1 3 0.00000 0.00000 18.68200
pm1boxcbswap: 0.00000
pm1cbswmt: 1.00000 1.00000
pmavb1: 0.00000
pmavb1in: 0.500000
pmavb1mt: 1.00000 1.00000
moltyp: 1 pmavb1ct: 1.000000 1.000000
moltyp: 2 pmavb1ct: 1.000000 1.000000
avb1rad: 1.00000
pmavb2: 0.00000
pmavb2in: 0.500000
pmavb2mt: 1.00000 1.00000
moltyp: 1 pmavb2ct: 1.000000 1.000000
moltyp: 2 pmavb2ct: 1.000000 1.000000
avb2rad: 1.00000
pmavb3: 0.00000
pmavb3mt: 1.00000 1.00000
moltyp: 1 pmavb3ct: 1.000000 1.000000
moltyp: 2 pmavb3ct: 1.000000 1.000000
avb3rad: 1.00000
pmcb: 0.00000
pmcbmt: 1.00000 1.00000
pmall: 1.00000 1.00000
pmback: 0.00000
pmbkmt: 1.00000 1.00000
pmpivot: 0.00000
pmpivmt: 1.00000 1.00000
pmconrot: 0.00000
pmcrmt: 1.00000 1.00000
pmcrback: 0.00000
pmcrbmt: 1.00000 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 1.00000
rmtraa: 0.500000
tatraa: 0.500000
pmtracm: 0.500000
pmtcmt: 1.00000 0.00000
rmtrac: 0.340000
tatrac: 0.500000
pmrotate: 1.00000
pmromt: 1.00000 0.00000
rmrot: 0.210000
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: default ideal
input_style: basic connectivity map
nunit: 4
nmaxcbmc: 4
lpdbnames: F
using the TIP4P force field
charge_assignment: manual
Building the input file for molecule type: 1
unit: 1 name:M charge: -1.04000
unit: 2 name:H charge: 0.52000
unit: 3 name:H charge: 0.52000
unit: 4 name:O charge: 0.00000
input_style: basic connectivity map
nunit: 6
nmaxcbmc: 6
lpdbnames: F
using the OPLS-aa force field
charge_assignment: manual
Building the input file for molecule type: 2
unit: 1 name:C n charge: 0.50000
unit: 2 name:HC~3 charge: 0.00000
unit: 3 name:O charge: -0.50000
unit: 4 name:N charge: -0.76000
unit: 5 name:H charge: 0.38000
unit: 6 name:H charge: 0.38000
Verifying input structures are consistent
Determining CBMC bond distributions
Determining cyclic subunits for molecule type 1
Determining cyclic subunits for molecule type 2
Default total charge on molecule 1 is 0.00000
Default total charge on molecule 2 is 0.00000
Total charge in the simulation system: 0.00000
Bond Types
Type: 1 Style: Fixed Length: 0.9572
Type: 2 Style: Fixed Length: 0.1500
Type: 7 Style: Standard Harmonic Length: 1.3350 Constant: 246576.1
Type: 11 Style: Standard Harmonic Length: 1.2290 Constant: 286833.5
Type: 41 Style: Standard Harmonic Length: 1.0900 Constant: 171093.6
Type: 47 Style: Standard Harmonic Length: 1.0100 Constant: 218396.0
Angle Types
Type: 1 Style: Fixed Angle Angle: 104.520
Type: 2 Style: Fixed Angle Angle: 52.260
Type: 4 Style: Standard Harmonic Angle: 120.000 Constant: 17612.6
Type: 71 Style: Standard Harmonic Angle: 122.900 Constant: 40257.3
Type: 126 Style: Standard Harmonic Angle: 115.000 Constant: 20128.7
Type: 147 Style: Standard Harmonic Angle: 119.800 Constant: 17612.6
Torsion Types
Type: 51 Style: OPLS Cosine Series
k1: 0.0 k2: 1232.9 k3: 0.0
with 1-4 vdw and scaled (0.500) 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
Coulombic inter- and intra-molecular interactions
including the real-space terms up to half the shortest box length
Molecular mass for molecule type 1 is 18.0148 g/mol
Molecular mass for molecule type 2 is 45.0407 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 0.05353 0.00000 0.00000
Box idim hinverse: 1 2 0.00000 0.05353 0.00000
Box idim hinverse: 1 3 0.00000 0.00000 0.05353
Finished initconf
Energies exclusively from internal potentials
Nonbonded Force Field
Soft Core Lennard Jones potential
u(r) = 4*epsilon[1/(alpha(1-lambda)^2*+(r/sigma)^6)^2 - 1/(alpha(1-lambda)^2+(r/sigma)^6)] - shift
alpha = 0.500000 lambda = 0.500000
Num. Atom(i) Num. Atom(j) sigma epsilon shift 1-4sig 1-4eps
1 H 1 H 0.000 0.000 0.000 0.000 0.000
1 H 2 O 0.000 0.000 0.000 0.000 0.000
1 H 3 M 0.000 0.000 0.000 0.000 0.000
1 H 7 C n 0.000 0.000 0.000 0.000 0.000
1 H 33 H 0.000 0.000 0.000 0.000 0.000
1 H 39 HC~3 0.000 0.000 0.000 0.000 0.000
1 H 49 N 0.000 0.000 0.000 0.000 0.000
1 H 58 O 0.000 0.000 0.000 0.000 0.000
2 O 2 O 3.154 78.020 0.000 0.000 0.000
2 O 3 M 0.000 0.000 0.000 0.000 0.000
2 O 7 C n 3.439 64.206 0.000 0.000 0.000
2 O 33 H 0.000 0.000 0.000 0.000 0.000
2 O 39 HC~3 2.763 24.267 0.000 0.000 0.000
2 O 49 N 3.201 81.697 0.000 0.000 0.000
2 O 58 O 3.055 90.801 0.000 0.000 0.000
3 M 3 M 0.000 0.000 0.000 0.000 0.000
3 M 7 C n 0.000 0.000 0.000 0.000 0.000
3 M 33 H 0.000 0.000 0.000 0.000 0.000
3 M 39 HC~3 0.000 0.000 0.000 0.000 0.000
3 M 49 N 0.000 0.000 0.000 0.000 0.000
3 M 58 O 0.000 0.000 0.000 0.000 0.000
7 C n 7 C n 3.750 52.838 0.000 3.750 26.419
7 C n 33 H 0.000 0.000 0.000 0.000 0.000
7 C n 39 HC~3 3.012 19.971 0.000 3.012 9.985
7 C n 49 N 3.491 67.232 0.000 3.491 33.616
7 C n 58 O 3.332 74.724 0.000 3.332 37.362
33 H 33 H 0.000 0.000 0.000 0.000 0.000
33 H 39 HC~3 0.000 0.000 0.000 0.000 0.000
33 H 49 N 0.000 0.000 0.000 0.000 0.000
33 H 58 O 0.000 0.000 0.000 0.000 0.000
39 HC~3 39 HC~3 2.420 7.548 0.000 2.420 3.774
39 HC~3 49 N 2.804 25.411 0.000 2.804 12.706
39 HC~3 58 O 2.676 28.243 0.000 2.676 14.121
49 N 49 N 3.250 85.547 0.000 3.250 42.773
49 N 58 O 3.102 95.080 0.000 3.102 47.540
58 O 58 O 2.960 105.675 0.000 2.960 52.838
Number of MC cycles: 1
Number of molecules: 217
Temperature [K]: 298.00000
Initial Energies for Box 1
Total molecules in this box 217
Molecules of type 1 : 216
Molecules of type 2 : 1
total vibration 299.965 [K] 0.59609 [kcal/mol]
regular 299.965 [K] 0.59609 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 150.164 [K] 0.29841 [kcal/mol]
regular 150.164 [K] 0.29841 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -11133.301 [K] -22.12427 [kcal/mol]
regular -11133.301 [K] -22.12427 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 159990.306 [K] 317.93527 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 159990.306 [K] 317.93527 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic -767569.378 [K] -1525.32603 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -618262.2454 [K] -1228.620529 [kcal/mol]
dU/d[lambda_lj] -105.064 [K] -0.20879 [kcal/mol]
dU/d[lambda_c] -10858.556 [K] -21.57830 [kcal/mol]
Foreign Lambda energy calculations (box 1)
index lambda_lj lambda_c Total Energy [K] Total Energy [kcal/mol]
1 1.000 1.000 -621754.0142 -1235.5594
2 0.501 0.499 -618251.4896 -1228.5992
3 0.500 0.500 -618262.2454 -1228.6205
4 0.499 0.501 -618272.9967 -1228.6419
5 0.000 0.000 -612763.4269 -1217.6932
initial virial pressure in box 1 = 14471734.28
+++++ start of markov chain +++++
Cycle Box Energy [K] Volume [A^3] Press. [kPa] dU/dl_lj dU/dl_c Molecul
Foreign energies, by lambda index
1 B: 1 -0.64454691E+06 0.65203E+04 14471734.3 -0.10718E+03 -0.11138E+05 216 1
fu: -0.648184E+06 -0.644536E+06 -0.644547E+06 -0.644558E+06 -0.638908E+06
+++++ end of markov chain +++++
Final hmatrix (general box dimensions)
Box: 1
hmatrix(1,x) 18.68200 0.00000 0.00000
hmatrix(2,x) 0.00000 18.68200 0.00000
hmatrix(3,x) 0.00000 0.00000 18.68200
* COM Translation Moves *
Molecule: 1 Box: 1 Attempts: 113. Accepted: 56. Accepted: 49.558 %
* Rotation Moves *
Molecule: 1 Box: 1 Attempts: 104. Accepted: 63. Accepted: 60.577 %
Final Energies for Box 1
Total molecules in this box 217
Molecules of type 1 : 216
Molecules of type 2 : 1
total vibration 299.965 [K] 0.59609 [kcal/mol]
regular 299.965 [K] 0.59609 [kcal/mol]
bond-bond(1-2) 0.000 [K] 0.00000 [kcal/mol]
total angle 150.164 [K] 0.29841 [kcal/mol]
regular 150.164 [K] 0.29841 [kcal/mol]
angle-angle 0.000 [K] 0.00000 [kcal/mol]
total torsion -11133.301 [K] -22.12427 [kcal/mol]
regular -11133.301 [K] -22.12427 [kcal/mol]
improper 0.000 [K] 0.00000 [kcal/mol]
total nonbond 160890.750 [K] 319.72465 [kcal/mol]
intramolecular 0.000 [K] 0.00000 [kcal/mol]
2-body nonbond 160890.750 [K] 319.72465 [kcal/mol]
3-body nonbond 0.000 [K] 0.00000 [kcal/mol]
total coulombic -794754.484 [K] -1579.34870 [kcal/mol]
external field 0.000 [K] 0.00000 [kcal/mol]
solvation 0.000 [K] 0.00000 [kcal/mol]
total classical -644546.9062 [K] -1280.853824 [kcal/mol]
dU/d[lambda_lj] -107.179 [K] -0.21299 [kcal/mol]
dU/d[lambda_c] -11138.291 [K] -22.13419 [kcal/mol]
Foreign Lambda energy calculations (box 1)
index lambda_lj lambda_c Total Energy [K] Total Energy [kcal/mol]
1 1.000 1.000 -648183.8869 -1288.0813
2 0.501 0.499 -644535.8729 -1280.8319
3 0.500 0.500 -644546.9062 -1280.8538
4 0.499 0.501 -644557.9351 -1280.8757
5 0.000 0.000 -638908.0065 -1269.6481
Averages Units Type Box 1
Volume nm^3 0.65203E+01
Volume^2 nm^6 0.42515E+02
Molecule Number 1 216.000
Molecule Number 2 1.000
Molar Volume ml/mol 0.18095E+02
Specific Density g/ml 1.00246033
Number Density nm-3 1 33.12712
Number Density nm-3 2 0.15337
Mole Fraction 1 0.9953917
Mole Fraction 2 0.0046083
Radius of Gyration A 1 0.3135314
Radius of Gyration A 2 1.0692266
dU/d[lambda_lj] [K] -.10929E+03
dU/d[lambda_c] [K] -.10969E+05
Ideal Pressure kPa 0.13697E+06
Ideal p_i <N/V>kT kPa 1 0.13634E+06
Ideal p_i <N/V>kT kPa 2 0.63119E+03
Total Classical K -0.6304E+06
Inter vdw K 0.1600E+06
Angle K 0.1502E+03
Torsion K -0.1113E+05
Intra vdw K 0.0000E+00
External Field K 0.0000E+00
Vibration K 0.3000E+03
Coulomb K -0.7797E+06
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 -0.5241E+04
C_v: T^2<H^2>-<H>^2 J/K mol 0.6025E+04
Please see towhee_citations for a list of suggested citations for this simulation
