[gmx-developers] XVG Energy Discrepancies Between GROMACS Versions

[Mark Abraham]

Hi,

Thanks for the report! There was at least one relevant bug fix in 2018.4 -
see
http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html.
But doubtless there is more to investigate here.

Mark

On Tue, Jan 29, 2019 at 5:46 PM Miroslav Suruzhon <ms2m18 at soton.ac.uk>
wrote:

> 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). For example, showing only the first few timesteps for one
> of the perturbations for all versions of GROMACS since 2018.1 (except
> 2018.2):
>
> XVG:
>
> @ s0 legend "dH/d\xl\f{} fep-lambda = 0.0000"
> @ s1 legend "dH/d\xl\f{} mass-lambda = 0.0000"
> @ s2 legend "dH/d\xl\f{} vdw-lambda = 1.0000"
> @ s3 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 1.0000)"
> @ s4 legend "\xD\f{}H \xl\f{} to (0.2000, 0.0000, 1.0000)"
> @ s5 legend "pV (kJ/mol)"
>
>
> 2018.1:
>
> 0.0000 -174.60474 20.225147 277.66620 1.9073486e-05 -3.2027580 3.9291420
> 0.5000 -82.147018 8.3129530 236.27664 1.5258789e-05 -1.2502190 3.9439571
> 1.0000 -156.04514 11.252308 204.58133 7.6293945e-06 -2.5048264 3.9501503
>
>
> 2018.3:
>
> 0.0000 -174.61128 20.225662 277.66617 0.0000000 -3.2027481 3.9291420
> 0.5000 -82.146118 8.3130722 236.27664 1.5258789e-05 -1.2502289 3.9439571
> 1.0000 -156.04543 11.252201 204.58139 1.5258789e-05 -2.5047165 3.9501503
>
>
> 2018.4:
>
> 0.0000 -174.61128 20.225662 277.66617 2.6702881e-05 -34.366931 3.9291420
> 0.5000 -82.146118 8.3130722 236.27664 -2.2888184e-05 -16.014955 3.9439571
> 1.0000 -156.04543 11.252201 204.58139 -1.5258789e-05 -30.665316 3.9501503
>
>
> 2018.5:
>
> 0.0000 -174.61128 20.225662 277.66617 0.0000000 -34.366950 3.9291420
> 0.5000 -82.146126 8.3130722 236.27664 0.0000000 -16.014955 3.9439571
> 1.0000 -156.04543 11.252201 204.58139 0.0000000 -30.665323 3.9501503
>
>
> 2019:
>
> 0.0000 -18.344168 0.0000000 277.66617 1.1444092e-05 -3.1135101
> 0.5000 -7.9936657 0.0000000 236.27664 0.0000000 -1.1844406
> 1.0000 -15.156097 0.0000000 204.58139 3.0517578e-05 -2.4874344
>
>
> Ignoring the floating point errors, we can see that 2018.1 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 (not shown here,
> but the other .xvg files exhibit the same behaviour).  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 and 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 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 with the same
> libraries), 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. I have not uploaded any files but if any
> more information is required, I am happy to provide it.
>
>
> Thank you very much.
>
>
> Kind regards,
>
> Miroslav
>
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