AMBER Archive (2005)

Subject: AMBER: PB dynamics

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Wed Jan 12 2005 - 04:06:33 CST

Experience is what you get when you don't get what you
want.

                      -- Dan Stanford--

Dear List,

Im interested in performing a MD simulation where the
point key is to understand the effect of the solvent
molecules ( n-hexane) in the stability between two
complexes. I would like to know if the PB dynamics is
suitable for this kind of problem. I have solvated my
molecules with the option "solvatecap" in Xleap with the
n-hexane solvent. Can I carry out the PB dynamics with the
option igb=10 in sander and seting the value of the
external dielectric constant equal to the experimental
value for n-hexane?

Thanks in advance,

Best regards

Nelson Fonseca
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