On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
[EMAIL PROTECTED] 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
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Pascal Baillod (PhD student)
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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 [EMAIL PROTECTED]
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
http://md.chem.rug.nl/~periole
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