[gmx-developers] dEkin/dl parallelization issue

[Mark Abraham]

and/or test with an earlier version of the code?

Mark

On Thu, Dec 10, 2015 at 6:17 PM Berk Hess <hess at kth.se> wrote:

> On 12/10/2015 07:59 AM, Shirts, Michael R. (mrs5pt) wrote:
>
> > The work around is do not include fep-lambdas or mass-lambdas
> specification in mdp-file.
>
> Or explicitly setting the masses to be the same.  In virtually all cases
> of interest, there's a cancellation of the kinetic energy term (one is
> interested in  solvent alchemical change - ideal gas change or solvent
> alchemical change - protein complex alchemical change).
>
> I mean, the error shouldn't be there, but it's a very easy error to work
> around.
>
> This contribution also converges very quickly to its equilibrium value
> which is trivial to calculate.
>
> But I don't see any obvious bug in the code (but it's quite complex). Does
> this happen with MPI and/or thread parallelization?
> Could you file an issue redmine.gromacs.org and attach a tpr file that
> reproduces the problem?
>
> Cheers,
>
> Berk
>
>
> From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf
> of Igor Leontyev <ileontyev at ucdavis.edu>
> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Date: Wednesday, December 9, 2015 at 8:24 PM
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] dEkin/dl parallelization issue
>
> Hi.
> It looks there is a parallelization bug in computation of "dEkin/dl" term
> in free energy simulations.
> I simulate ddG with gromacs 5.1 and mixed topology, i.e. need dG in
> protein and in water:
>         ddG = dG(InProtein) - dG(InWater)
> The alchemical transformation involves only one atom mutation H->Cl. I
> expect that dEkin/dl terms InProtein and InWater cancel each other. But it
> is not always true.
>
> In 1 or 2 core simulations I get <dEkin/dl > value about 130 kJ/mol, for 4
> and 8 cores <dEkin/dl > drops down to ~ 65 kJ/mol and for 16 cores it drops
> down again about twice.
>
>
>
> Igor
>
>
>
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