[gmx-users] Enthapy of vaporization for aromatics

Eudes Fileti fileti at ufabc.edu.br
Thu Oct 8 22:32:35 CEST 2009


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.

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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