[gmx-developers] REMD based on prot pot ener: FINAL?

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Wed Mar 15 23:57:51 CET 2006


Sorry to annoy you all once again with this topic, and many thanks for all the
help! I think this could be my last one on this issue..

1) Using PME, I get the same protein potential energy with a) my new tgroup.c
routine and b) summing up g_energy protein potential energy terms (adding *0.5
where needed). But if I understood well, I am missing the reciprocal (lattice)
part of PME, for which there is only one term (epot[F_COUL_RECIP] or other???)
and no prot/other contributions written to separate variables. I neither count
it as a contribution with g_energy, nor with my new epotPROT routine in
tgroup.c. In both cases, I therefore assume I get the wrong potential energy for
prot bonded + (prot-prot + prot-solv) interactions. 

2) Can I "solve" this problem doing the MD with the generalized reaction field?
Is the result of the generalized reaction field calculation directly stored in
the epot[F_COUL_LR] term (which I can dissociate to prot and other
contributions), or do I have to add a new term?

3) Just to make it sure: the G96Bond and G96Angle terms that one can  choose to
print out with g_energy, as well as the epot[F_G96BONDS] and epot[F_G9ANGLES] of
tgroup.c, refer to the protein only? For solvent bonded term, gmx just adds up
the topological values by the number of solvent molecules, I guess?

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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