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<p>Hi.<br>
It looks there is a parallelization bug in computation of "dEkin/dl" term in free energy simulations.<br>
I simulate ddG with gromacs 5.1 and mixed topology, i.e. need dG in protein and in water:<br>
ddG = dG(InProtein) - dG(InWater)<br>
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.<br>
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<p>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.<br>
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<br>
The work around is do not include fep-lambdas or mass-lambdas specification in mdp-file.<br>
<br>
Igor<br>
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