[gmx-users] flexible organic solvents

Kukol, Andreas a.kukol at herts.ac.uk
Thu Aug 14 17:02:30 CEST 2008

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.


> -----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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