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Issue created by Paul Bauer@acmnpvMaintainer

Free energy discrepancies between GROMACS versions - Redmine #2849

Archive from user: Miroslav Suruzhon

Hello,

I was running some free energy perturbation simulations in GROMACS, and I had problems reproducing data from other people’s simulations in GROMACS. After several days of trying to find out the issue, I realised that different versions of GROMACS give very different results in the .xvg file for the same input .tpr file and .trr trajectory (using gmx mdrun -rerun). I have attached the relevant .tpr and .trr files for the first 5 ps for two lambda values, alongside with the .gro, .top and .mdp files I used to create the .tpr. I have also attached the .xvg files generated for every stable version of GROMACS since 2018.1.

Ignoring the floating point errors, we can see that 2018.1, 2018.2 and 2018.3 give more or less the same results, which are very different from those produced by 2018.4 and 2018.5, resulting in extremely large discrepancies in free energies - more than 20 kJ/mol using gmx bar. However, these discrepancies only seem to hold for the delta H values and not dH/dl. Finally, free energies calculated from 2019 using gmx bar seem to reproduce 2018.1 - 2018.3 but we can see that there is a missing column of data compared to other versions and most of the dH/dl derivatives do not agree with other versions of GROMACS.

Note that this issue only seems to persist when perturbing the Coulomb / bonded interactions. Van der Waals perturbation energies seem consistent between versions (not shown here).

Since the only variable for all of these simulations is the GROMACS version (which was compiled on the same computer (Ubuntu 18.04.1) with the same libraries (cmake 3.10.2, Open MPI 2.1.1, gcc 7.3.0), I highly suspect that there is (at least one) bug with the free energy implementation of the code (or the output thereof). However, I am not sure which version gives the “correct” results. Any feedback would be highly appreciated.

Thank you very much.

Kind regards,

Miroslav

(from redmine: issue id 2849, created on 2019-01-30 by gmxdefault, closed on 2019-02-15)

Disallow rerun with perturbed masses or constraints

Since rerun no longer integrates, free-energy contributions due to
changing masses and constraints are no longer computed. Now rerun
exits with a fatal error when such a system is provided.

Fixes #2849

Change-Id: Ic1550fce22f68c573b52d6895e1e61398b671e51
  • Revision a741d07b by Berk Hess on 2019-02-15T09:35:41Z:
Fix mass Delta H double counting

With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.

Refs #2703
Fixes #2849

Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c
  • Revision 499ab90c by Berk Hess on 2019-02-20T08:00:18Z:
Fix mass Delta H double counting

With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.

Refs #2703
Fixes #2849

Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c