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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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