[gmx-users] flexible organic solvents
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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