[gmx-users] Please rectify free energy problem

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 30 19:00:35 CEST 2011

On 30/08/2011 11:52 PM, pawan raghav wrote:
> g_lie calculates the deltaG= alpha(<Vl-s LJ>p - <Vl-s LJ>w) + 
> beta(<Vl-s el>p - <Vl-s el>w) equation. But when calculating DGbind 
> from g_lie it will ask for only one term at a time i.e. -Elj for 
> either <Vl-s LJ>p or <Vl-s LJ>w and -Eqq for either <Vl-s el>p  or 
> <Vl-s el>w. My question is when using only <Vl-s LJ>p for -Elj 
> and Vl-s el>p for  -Eqq, how the LJ and EL terms calculated for 
> ligand-water interaction or in vice-versa condition for ligand-protein 
> interactions to complete the deltaG equation?

This is at least the third time you've asked the same question. Perhaps 
the problem is with the question, and not with the people who are 
choosing not to answer it? I expect people find the notation a barrier 
to understanding the question, particularly when it contains at least 
one typographical error. Notation is a two-edged tool - one wishes to 
use it to facilitate comprehension, not impede it.

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