Re: [AMBER] Problem in nmode analysis of single water molecule by MMPBSA.py

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 24 Sep 2012 09:05:12 -0400

On Mon, Sep 24, 2012, Jason Swails wrote:
>
> You could try a flexible water model and see if that gives you better
> answers, but I would not expect it.

I *would* expect better behavior, as illustrated in the paper below. Doing
simple tests like this is to be encouraged, since it promotes a detailed
understanding of what is going on in normal mode calculations.

%A F. Paesani
%A W. Zhang
%A D.A. Case
%A T.E. Cheatham
%A G.A. Voth
%T An accurate and simple quantum model for liquid water
%J J. Chem. Phys.
%V 125
%P 184507
%D 2006

...good luck....dac


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Received on Mon Sep 24 2012 - 06:30:02 PDT
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