[gmx-users] Enthapy of vaporization for aromatics
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 9 08:23:48 CEST 2009
Eudes Fileti wrote:
> Hello gmx users.
> I have tried to calculate the enthalpy of vaporization of
> toluene liquid, which is about 38kJ/mol (exp. value) using
> the OPLS-UA model (7 sites). I generated the toluene topology
> adapting a template provided by PRODRG. I have obtained acceptable
> value for density and structure of the liquid, but for the enthalpy
> the value is much lower than expected; 18kJ/mol.
How long did you simulate in the gas-phase? Are the temperatures
identical? Did you use a short-enough time step, seeing that you do not
use constraints?
Often 5-10 ns gas-phase simulation are needed.
>
> I know there are subtleties in the treatment of aromatic systems.
> At Gmx users list I found some tips (see for example
> http://oldwww.gromacs.org/pipermail/gmx-developers/2009-January/002965.html
> ),
> but still I can not solve the problem.
>
> I already tried numerous ways to circumvent this problem
> and none worked well. It seems to me the problem may lie
> in the definition of the dihedrals.
>
> Below is the topology that I have used and the main simulation
> parameters used. If someone can help me I would be very grateful.
> Bests
> eef
>
> **** toluene.itp ****
> [ moleculetype ]
> ; Name nrexcl
> TOL 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 opls_067 1 TOL CH3 1 0.000 15.0350
> 2 opls_076 1 TOL CB 1 0.000 12.0110
> 3 opls_075 1 TOL CD 1 0.000 13.0190
> 4 opls_075 1 TOL CD 1 0.000 13.0190
> 5 opls_075 1 TOL CD 1 0.000 13.0190
> 6 opls_075 1 TOL CD 1 0.000 13.0190
> 7 opls_075 1 TOL CD 1 0.000 13.0190
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 1 0.153 334720.0 0.153 334720.0 ; CH3 CB
> 2 3 1 0.141 418400.0 0.141 418400.0 ; CB CD
> 2 7 1 0.141 418400.0 0.141 418400.0 ; CB CD
> 3 4 1 0.141 418400.0 0.141 418400.0 ; CD CD
> 4 5 1 0.141 418400.0 0.141 418400.0 ; CD CD
> 5 6 1 0.141 418400.0 0.141 418400.0 ; CD CD
> 6 7 1 0.141 418400.0 0.141 418400.0 ; CD CD
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 1 120.0 418.4 120.0 418.4 ; CH3 CB
> CD
> 1 2 7 1 120.0 418.4 120.0 418.4 ; CH3 CB
> CD
> 3 2 7 1 120.0 418.4 120.0 418.4 ; CD CB CD
> 2 3 4 1 120.0 418.4 120.0 418.4 ; CB CD CD
> 3 4 5 1 120.0 418.4 120.0 418.4 ; CD CD CD
> 4 5 6 1 120.0 418.4 120.0 418.4 ; CD CD CD
> 5 6 7 1 120.0 418.4 120.0 418.4 ; CD CD CD
> 2 7 6 1 120.0 418.4 120.0 418.4 ; CB CD CD
>
>
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 2 7 3 1 2 0.0 1673.6 ; imp CB CD
> CD CH3
> 2 3 4 5 1 180.0 12.9704 2 ; imp CB CD
> CD CD
> 3 4 5 6 1 180.0 12.9704 2 ; imp CD CD
> CD CD
> 4 5 6 7 1 180.0 12.9704 2 ; imp CD CD
> CD CD
> 5 6 7 2 1 180.0 12.9704 2 ; imp CD CD
> CD CB
> 6 7 2 3 1 180.0 12.9704 2 ; imp CD CD
> CB CD
> 7 2 3 4 1 180.0 12.9704 2 ; imp CD CB
> CD CD
>
>
> **** toluene.mdp ****
> integrator = md
> nstlist = 5
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> domain-decomposition = no
> coulombtype = Cut-off
> rcoulomb-switch = 0
> rcoulomb = 1.2
> vdw-type = Cut-off
> rvdw-switch = 0
> rvdw = 1.2
> DispCorr = EnerPres
> table-extension = 1
> energygrp_table =
> fourierspacing = 0.12
> Tcoupl = berendsen
> tc-grps = System
> tau_t = 0.1
> ref_t = 300
> Pcoupl = No
> Pcoupltype = isotropic
> tau_p = 1
> compressibility = 5.0e-5
> ref_p = 1.1
> constraints = none
> constraint-algorithm = Lincs
> unconstrained-start = no
> energygrp_excl =
>
> **** toluene.gro ****
> PRODRG COORDS
> 7
> 1TOL CH3 1 0.159 -0.143 -0.050
> 1TOL CB 2 0.154 -0.227 0.078
> 1TOL CD 3 0.224 -0.349 0.084
> 1TOL CD 4 0.219 -0.426 0.203
> 1TOL CD 5 0.145 -0.379 0.313
> 1TOL CD 6 0.075 -0.256 0.308
> 1TOL CD 7 0.080 -0.180 0.189
> 0.51300 0.51300 0.51300
>
>
>
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4437-0196
> http://fileti.ufabc.edu.br
>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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