AMBER Archive (2009)

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

From: ranga nath (ranganath71_at_gmail.com)
Date: Sat Mar 21 2009 - 21:04:13 CDT

thank you Dr. David for the references.

ranga

On Fri, Mar 20, 2009 at 1:38 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> 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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