[gmx-users] flexible organic solvents

[patrick fuchs]

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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of Sascha Rehm
>> Sent: 14 August 2008 12:03
>> To: gmx-users at 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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-- 
_________________________________________________________________
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Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INTS, INSERM UMR-S726, Université Paris Diderot,
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