[gmx-users] flexible organic solvents

Sascha Rehm SaschaRehm at gmx.de
Thu Aug 14 13:02:45 CEST 2008

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,


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