[gmx-developers] FW: XVG Energy Discrepancies Between GROMACS Versions

Wed Jan 30 11:17:30 CET 2019

Thank you everyone for the replies. I also think something might have been broken (or fixed!) by the 2018.4 update. I have created a new issue in redmine.

Miroslav

On 29/01/2019 21:38, Michael R Shirts wrote:
I am happy to take a look, but please submit an issue (with exactly this information) and upload the files you used!

Best,
~~~~~~~~~~~~~~~~
Michael Shirts
Associate Professor
michael.shirts at colorado.edu<mailto:michael.shirts at colorado.edu>
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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 Mark Abraham <mark.j.abraham at gmail.com><mailto:mark.j.abraham at gmail.com>
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: Tuesday, January 29, 2019 at 10:38 AM
To: "gmx-developers at gromacs.org"<mailto:gmx-developers at gromacs.org> <gmx-developers at gromacs.org><mailto:gmx-developers at gromacs.org>
Cc: "gromacs.org_gmx-developers at maillist.sys.kth.se"<mailto:gromacs.org_gmx-developers at maillist.sys.kth.se> <gromacs.org_gmx-developers at maillist.sys.kth.se><mailto:gromacs.org_gmx-developers at maillist.sys.kth.se>
Subject: Re: [gmx-developers] XVG Energy Discrepancies Between GROMACS Versions

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<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2018.4%2Frelease-notes%2F2018%2F2018.4.html&data=01%7C01%7CM.Suruzhon%40soton.ac.uk%7Ca64f5f16ee4f452d537308d6863228a0%7C4a5378f929f44d3ebe89669d03ada9d8%7C1&sdata=Pz7qxPV%2FbGPZp6HyVuo0LVy2i56iaQaZs2omdaHOZSw%3D&reserved=0>. 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<mailto: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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