AMBER Archive (2004)

Subject: AMBER: Implicit Solvent Models

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Thu Dec 09 2004 - 06:02:10 CST

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

                      -- Dan Stanford--

Dear all,

I want to perform some simple MD runs of of two small
molecules solvated in hexane. To speed up the calculations
can I use the implicit solvent model implemented in AMBER
8, setting the paramater relative to the dielectric
constant equal to the value of hexane? As Im not
interested in computing Free-energies of solvation, only
interested in some structural information, does I need to
scale the atomic radiis of the atoms? Is the model of GB
suitable for non-water solvents?

Thanks in advance to all.

Nelson Fonseca
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