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

[Yang Ye]

hi, pascal

Would you like to take a look at this recent articles on JCTC?

http://dx.doi.org/10.1021/ct050196z

@article{OkurA._ct050196z,
author = {Okur, A. and Wickstrom, L. and Layten, M. and Geney, R. and 
Song, K. and Hornak, V. and Simmerling, C.},
title = {Improved Efficiency of Replica Exchange Simulations through Use 
of a Hybrid Explicit/Implicit Solvation Model},
journal = {Journal of Chemical Theory and Computation},
volume = {2},
number = {2},
pages = {420-433},
year = {2006},
URL = {http://dx.doi.org/10.1021/ct050196z}
}

}

Yang Ye

pascal.baillod at epfl.ch wrote:
> Hi!
>
> 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
>
>
> *******************************************************************************
> 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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