[gmx-users] A simulation of pure chloroform with AMBER compatible parameters never gives the right density

[David van der Spoel]

On 2011-12-20 15:03, anaome at fundp.ac.be wrote:
> 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

Haven't tried that one, but we have OPLS/AA and GAFF, see:
http://virtualchemistry.org/molecules/67-66-3/index.php
for those the density is too low as well.

>
> 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
> ++++++++++++++++++++
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se