[gmx-users] Three-site model for acetonitrile
christoph.freudenberger at chemie.uni-ulm.de
Mon Feb 24 10:56:20 CET 2003
I got into trouble looking for an apropriate model for acetonitrile
to use in gromacs.
I checked three potentials from the literatur by doing some short
simulations, finding them to give similar results, so i decided to
use the following for my system.
E. Guardia, Mol. Simul., 26, 2001, 287;
The parameters given there are:
eps (KJ/mol) sig(A) q(e)
Me 0.7824 3.775 0.206
C 0.544 3.650 0.247
N 0.6276 3.200 -0.453
Here is what i converted them to for my .itp:
[ atomtypes ]
;type mass charge ptype c6 c12
MeAN 15.03500 0.000 A 0.90571E-02 0.26212E-04 ;
CAN 12.01100 0.000 A 0.51454E-02 0.12167E-04 ;
NAN 14.00670 0.000 A 0.26955E-02 0.28943E-05 ;
[ moleculetype ]
; name nrexcl
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 MeAN 1 MeCN C1AN 1 0.206 15.035
2 CAN 1 MeCN C2AN 1 0.247 12.011
3 NAN 1 MeCN N3AN 1 -0.453 14.007
The problem is, that the system "freezes" in longterm simulations.
The molecules do not move anymore (except some minor oszillations)
as if the viscosity of the system was extremly high.
I figured that the density of the system (950g/l) might be to high,
so I changed the LJ-Parameters a little bit, to accieve better
agreement with the expt. density. First every thing looked fine
but again in a longterm simulation the system froze to a cystal-like
behavior, although the density remained constant at the new value
Can you give me a hint, what is wrong here?
Do you know a set of parameters for MeCN that works with gromacs?
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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