AMBER Archive (2009)

Subject: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box

From: ranga nath (
Date: Wed Mar 18 2009 - 23:27:54 CDT

I am thinking to study folding dynamics of a small peptide at the interphase
of water/oil, if it is feasible. I can see solvent boxes of only one type of
solvents like water, methanol.

Can you please help me to get started:

First of all, Is it possible using AMBER10?
If yes, are there any equilibrated boxes available?
If no, what are the pit falls I should be aware of while setting up such
thank you in advance for your help.
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