Dear Users,
I am trying to reproduce the results obtained by Fox & Kollman on
chloroform presented in the following papers but can never achieve the
proper density of 1.459 they obtain with their own rigid CHCL3 model.
The best I obtain with the parameters presented below is 1.390. I
tried with both version 4.5.3 and 4.0.7.
Can anyone help me on that ?
Thank you
Aymeric Naômé
The Journal of Physical Chemistry, 1996, 100, 25, 10779-10783
The Journal of Physical Chemistry B, 1998, 102, 41, 8070-8079
The parameters are:
qC=-0.345 eps=0.1094 kcal/mol R*=1.908 Ang.
qCl=0.012 eps=0.2550 R*=2.000
qH=0.309 eps=0.0157 R*=1.187
C-Cl=1.758 Ang.
C-H=1.100
H-C-Cl=107.7°
Cl-C-Cl=112.2°
And my corresponding topology file is the following:
sigma=2*(R*/10)/(2^(1/6))
epsilon=eps*4.184
++++++++++++++++++++
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 0.5 0.8333
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01
H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02
Cl 17 35.453 0.0000 A 3.56359e-01 1.10669e+00
[ moleculetype ]
; Name nrexcl
CHCL3 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CT 1 CHCL3 C 1 -0.345 12.011
; qtot -0.386
2 H3 1 CHCL3 H 1 0.309 1.008
; qtot -0.120
3 Cl 1 CHCL3 Cl1 1 0.012 35.453
; qtot -0.080
4 Cl 1 CHCL3 Cl2 1 0.012 35.453
; qtot -0.040
5 Cl 1 CHCL3 Cl3 1 0.012 35.453
; qtot 0
[ constraints ]
1 3 1 0.1758
1 4 1 0.1758
1 5 1 0.1758
1 2 1 0.1100
; 2 3 2 0.2340
2 4 2 0.2340
2 5 2 0.2340
3 4 2 0.2901
4 5 2 0.2901
5 3 2 0.2901
[ system ]
; Name
CHCl3_256
[ molecules ]
; Compound #mols
CHCL3 256
++++++++++++++++++++
The simulation parameters in the first paper:
MD program: AMBER 4.1
200-300 molecules
dt=2fs (rigid model)
cut-off=12 Ang.
long range correction according to Allen&Tildesley
Berendsen thermostat with coupling constant 0.4 ps-1
temperature=300 K
inverse compressibility 1.086 10-4 bar-1
Berendsen barostat with coupling constant 0.2 ps-1
pressure=1 atm
SHAKE constraint solver
Below is my mdp file with the corresponding parameters:
++++++++++++++++++++
title = CHCl3_box
cpp = /lib/cpp -traditional
define =
constraints =
integrator = md
dt = 0.002 ; fs !
nsteps = 400000 ; total 10000 ps.
nstcomm = 1
nstxout = 500
nstvout = 1000
nstfout = 0
nstlog = 500
nstenergy = 500
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = cut-off
rcoulomb = 1.2
rvdw = 1.2
DispCorr = EnerPres
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
energygrps = CHCL3
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 5
tc_grps = CHCL3
ref_t = 300
; Pressure coupling is on
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 2.5
compressibility = 10.86e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Energy group exclusion
energygrp_excl =
freezegrps =
freezedim =
; Non-equilibrium Thermodynamics
acc_grps =
accelarate =
; center of mass
comm_mode = linear
comm_grps =
; Type of constraint algorithm
constraint-algorithm = Shake
++++++++++++++++++++
--
Aymeric Naômé
Ph. D. Student
UCPTS Division
University of Namur
61 Rue de Bruxelles
5000 Namur
BELGIUM
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