[gmx-users] Contribution to total potential energy given by protein in PME md

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Tue Mar 21 14:34:20 CET 2006


I am trying to compute the contribution to the potential energy given by a
protein, in an explicit water simulation. I defined two energy groups, "protein"
and "other". I use g_energy and sum up all the bonded terms (as waters are not
counted in those), all prot-prot non-bonded terms and all protein-solvent
non-bonded terms. I use PME for long-range electrostatics. 

1) From what I read in some archives, the reciprocal term of the PME summation
is not counted in the coul-LR term..? so I guess there's no way to correctly
compute protein potential energy using PME? 

2) Could I get a better approximation using Reaction Field (RF) for long range
electrostatics? Is the RF fully accounted for in coul-LR terms? 

Thank you very much for your help!


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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