AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Mar 19 2009 - 12:38:52 CDT

On Thu, Mar 19, 2009, ranga nath wrote:

> 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.

You might want to look at:

%A Y. Zhang
%A S.E. Feller
%A B.R. Brooks
%A R.W. Pastor
%T Computer simulation of liquid/liquid interfaces. I. Theory and
%application to octane/water
%J J. Chem. Phys.
%V 103
%P 10252-66
%D 1995

%A S.A. Patel
%A C.L. Brooks, III
%T Revisiting the hexane-water interface via molecular dynamics
%simulations using nonadditive alkane-water potentials
%J J. Chem. Phys.
%V 124
%P 204706/1-204706/14
%D 2006

Amber doesn't have much built-in support for getting started in this
area.

...dac

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