[gmx-users] Potential energy contributions and total pot ener (2)

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Wed Aug 15 21:44:15 CEST 2007

Dear community,

Thanks, Mark! But I can't find any g_energy or log file terms specifically
related to solvent bonded energy (bonds and angles). The log file bonded terms
are for the total system, I guess, but they are very close to the ones I get
when I request their "protein" counterpart from g_energy. My guess would be
that, in my 103-residue protein (1142 at) system solvated by 14'076 water
molecules (42'228 at), there should be a large difference between protein bonded
and solvent bonded terms.

Perhaps water bonded terms are not counted at all, as the water molecule
geometry dose not vary with the SPC model, during the simulation? 

By the way, is the assumption of my previous mail correct? The one on the total
potential energy formulation as a function of g_energy potential energy
decomposition terms:

Etot = a + 0.5*b + c (+ d), with

a) protein-protein (bonded and non-bonded)
b) protein-solvent (interaction, non-bonded)
c) solvent-solvent (interaction, non-bonded)
(d) solvent bonded terms)

(Of course this only holds when using a non-PME method (i.e. generalised
reaction field) for long range electrostatics!)

Thank you very much for any info!!


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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