[gmx-developers] dEkin/dl parallelization issue

Igor Leontyev ileontyev at ucdavis.edu
Thu Dec 10 07:33:53 CET 2015

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.

The work around is do not include fep-lambdas or mass-lambdas specification in mdp-file.

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