[gmx-users] FEP and loss of performance

Chris Neale chris.neale at utoronto.ca
Mon Apr 4 18:44:42 CEST 2011

 >> Dear Chris and Justin

>>/  Thank you for your precious suggestions
/>>/  This is a test that i perform in a single machine with 8 cores
/>>/  and gromacs 4.5.4.
/>>/  I am trying  to enhance the  sampling of a protein using the decoupling scheme
/>>/  of the free energy module of gromacs.  However when i decouple only the
/>>/  protein, the protein collapsed. Because i simulated in NVT i thought that
/>>/  this was an effect of the solvent. I was trying to decouple also the solvent
/>>/  to understand the system behavior.
>Rather than suspect that the solvent is the problem, it's more likely that
>decoupling an entire protein simply isn't stable.  I have never tried anything
>that enormous, but the volume change in the system could be unstable, along with
>any number of factors, depending on how you approach it.
>If you're looking for better sampling, REMD is a much more robust approach than
>trying to manipulate the interactions of huge parts of your system using the
>free energy code.

Presumably Luca is interested in some type of hamiltonian exchange where lambda represents the interactions between the protein and the solvent?
This can actually be a useful method for enhancing sampling. I think it's dangerous if we rely to heavily on "try something else". I still see no methodological
reason a priori why there should be any actual slowdown, so that makes me think that it's an implementation thing, and there is at least the possibility that this is
something that could be fixed as an enhancement.



>/   I expected a loss of performance, but not so drastic.
/>/  Luca
/>>/  Load balancing problems I can understand, but why would it take longer
/>>/  in absolute time? I would have thought that some nodes would simple be
/>>/  sitting idle, but this should not cause an increase in the overall
/>>/  simulation time (15x at that!).
/>>/  There must be some extra communication?
/>>/  I agree with Justin that this seems like a strange thing to do, but
/>>/  still I think that there must be some underlying coding issue (probably
/>>/  one that only exists because of a reasonable assumption that nobody
/>>/  would annihilate the largest part of their system).
/>>/  Chris.
/>>/  Luca Bellucci wrote:
/>>>/  /  Hi Chris,
/>>/  />/  thank for the suggestions,
/>>/  />/  in the previous mail there is a mistake because
/>>/  />/  couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
/>>/  />/  Now the problem of the load balance seems reasonable, because
/>>/  />/  the water box is large ~9.0 nm.
/>>/  /
/>>/  Now your outcome makes a lot more sense.  You're decoupling all of the
/>>/  solvent? I don't see how that is going to be physically stable or terribly

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