[gmx-developers] dEkin/dl parallelization issue

[Shirts, Michael R. (mrs5pt)]

> 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.

From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>> on behalf of Igor Leontyev <ileontyev at ucdavis.edu<mailto:ileontyev at ucdavis.edu>>
Reply-To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>>
Date: Wednesday, December 9, 2015 at 8:24 PM
To: "gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>" <gmx-developers at gromacs.org<mailto: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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