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
[EMAIL PROTECTED] 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 [EMAIL PROTECTED]
Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
CH-1015 Lausanne
*******************************************************************************
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