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

[Xavier Periole]

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	
> *******************************************************************************
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------