[gmx-users] Total potential energy: 1/2 protein-solvent interactions??

Xavier Periole X.Periole at rug.nl
Thu Mar 6 08:46:15 CET 2008

On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
  pascal.baillod at epfl.ch wrote:
> Dear developers,
> I would like to know the exact definition of the total potential energy with
> respect to protein-solvent interactions, in an explicit solvent protein 
> simulation.
The definition of protein-solvent interaction is the sum of the
pair-wise interaction (non-bonded) involving on one side the protein
atoms and on the other side the solvent atoms.

> For protein atom Pm and solvent atom Wn, there are two interactions:
> Pm to Wn
> Wn to Pm
Those two terms are identical! You can not separate them! Here you just
express them in two different ways which are totally identical.
It is like A+B=B+A, can you differentiate the sum of B on A and the
sum of A on B?
> Are both interaction energies counted in the total potential energy given in 
> the log file or by g_energy?
As they are the same they are both counted but only one time!
> If I want to compute the total potential enery of the protein, plus
> protein-solvent interactions, should I then only add half of the 
> protein-solvent terms given by g_energy? I am only interested in 
> the effect of solvent "felt" by the protein, and not in the effect 
> of the protein felt by the solvent.
Again, how would you differentiate those two terms? Counting
the interactions from protein to solvent or solvent to protein is
exactly the same.
> Thank you very much for your help!
> Pascal 
> *******************************************************************************
> Pascal Baillod (PhD student) 
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and 
>Biochemistry	pascal.baillod at epfl.ch
> Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
> CH-1015 Lausanne	
> *******************************************************************************
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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