Hi,
additionally to the remaks of Andreas there are some parameters in the
GROMOS force field G53a5/6 for the solvents you want to simulate (see
the original paper). A good read of chapter five of the manual and to
all the files in the $GMX/share/top directory should let you build those
models. Note there's also a decane.itp there, which uses the
Ryckaert-Bellemans potential (as in Berger lipids).
One comment on the chair to boat (or more exactly twist-boat)
transition, the enthalpy barrier has been estimated to ~ 10 kcal/mol by
ab initio and MM2 calculations. It is thus unlikely to observe any
transition within a few nanoseconds if you start from a chair
conformation at room temperature.
Ciao,
Patrick
Kukol, Andreas a écrit :
Yes that should be possible without big problems. The Gromacs manual and Wiki
pages about how to build a topology is a good starting point.
Then you could try the gromacs program x2top to generate a topology, or the
Prodrg2 server.
Andreas
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Sascha Rehm
Sent: 14 August 2008 12:03
To: gmx-users@gromacs.org
Subject: [gmx-users] flexible organic solvents
Dear Gromacs users,
I simulate proteins with different organic solvents like toluene,
cyclohexane or isopentane. Right now, I used rigid body models for these
solvents, made and simulated with Amber. For my future work, I unse
Gromacs and need to rebuild these solvents.
Can I build a cyclohexane model, which is more flexible and can change
from chair conformation to boat conformation and vice versa? And how do
I build a non-rigid Isopentane with internal degrees of freedom?
Hope, this is not a stupid questions, but I searched quite a while the
mailing list and also google, but did nearly find nothing about other
common (flexible) solvents.
Can someone give me a hint, which keywords I should use to search or
where I can find some informations/tutorials/explanations?
Thanks a lot,
Sascha
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Patrick FUCHS
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