[gmx-developers] dEkin/dl parallelization issue

Berk Hess hess at kth.se
Thu Dec 10 08:17:35 CET 2015

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?


> 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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