[gmx-users] FEP and loss of performance

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Apr 5 23:35:15 CEST 2011

I don't know if it is possible or not. I think that you can enhance  
your chances of developer attention if you develop a small and simple  
test system that reproduces the slowdown and very explicitly state  
your case for why you can't use some other method. I would suggest  
posting that to the mailing list and, if you don't get any response,  
post it as an enhancement request on the redmine page (or whatever has  
taken over from bugzilla).

Good luck,

-- original message --

Yes i am testing the possibility to perform an Hamiltonian-REMD
Energy barriers can be overcome  increasing the temperature system or scaling
potential energy  with a lambda value, these methods are "equivalent".
Both have advantages and disavantages, at this stage it is not the right place
to debate on it. The main problem seems to be how to overcome to the the loss
of gromacs performance in such calculation.  At this moment it seems an
intrinsic code problem.
Is it possible?

>  >> 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.
> Chris.
> -Justin
> >/   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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