<div dir="ltr">Hi,<div><br></div><div>Thanks for the report! There was at least one relevant bug fix in 2018.4 - see <a href="http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html">http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html</a>. But doubtless there is more to investigate here.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jan 29, 2019 at 5:46 PM Miroslav Suruzhon <<a href="mailto:ms2m18@soton.ac.uk">ms2m18@soton.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
I was running some free energy perturbation simulations in GROMACS, and <br>
I had problems reproducing data from other people's simulations in <br>
GROMACS. After several days of trying to find out the issue, I realised <br>
that different versions of GROMACS give very different results in the <br>
.xvg file for the same input .tpr file and .trr trajectory (using gmx <br>
mdrun -rerun). For example, showing only the first few timesteps for one <br>
of the perturbations for all versions of GROMACS since 2018.1 (except <br>
2018.2):<br>
<br>
XVG:<br>
<br>
@ s0 legend "dH/d\xl\f{} fep-lambda = 0.0000"<br>
@ s1 legend "dH/d\xl\f{} mass-lambda = 0.0000"<br>
@ s2 legend "dH/d\xl\f{} vdw-lambda = 1.0000"<br>
@ s3 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 1.0000)"<br>
@ s4 legend "\xD\f{}H \xl\f{} to (0.2000, 0.0000, 1.0000)"<br>
@ s5 legend "pV (kJ/mol)"<br>
<br>
<br>
2018.1:<br>
<br>
0.0000 -174.60474 20.225147 277.66620 1.9073486e-05 -3.2027580 3.9291420<br>
0.5000 -82.147018 8.3129530 236.27664 1.5258789e-05 -1.2502190 3.9439571<br>
1.0000 -156.04514 11.252308 204.58133 7.6293945e-06 -2.5048264 3.9501503<br>
<br>
<br>
2018.3:<br>
<br>
0.0000 -174.61128 20.225662 277.66617 0.0000000 -3.2027481 3.9291420<br>
0.5000 -82.146118 8.3130722 236.27664 1.5258789e-05 -1.2502289 3.9439571<br>
1.0000 -156.04543 11.252201 204.58139 1.5258789e-05 -2.5047165 3.9501503<br>
<br>
<br>
2018.4:<br>
<br>
0.0000 -174.61128 20.225662 277.66617 2.6702881e-05 -34.366931 3.9291420<br>
0.5000 -82.146118 8.3130722 236.27664 -2.2888184e-05 -16.014955 3.9439571<br>
1.0000 -156.04543 11.252201 204.58139 -1.5258789e-05 -30.665316 3.9501503<br>
<br>
<br>
2018.5:<br>
<br>
0.0000 -174.61128 20.225662 277.66617 0.0000000 -34.366950 3.9291420<br>
0.5000 -82.146126 8.3130722 236.27664 0.0000000 -16.014955 3.9439571<br>
1.0000 -156.04543 11.252201 204.58139 0.0000000 -30.665323 3.9501503<br>
<br>
<br>
2019:<br>
<br>
0.0000 -18.344168 0.0000000 277.66617 1.1444092e-05 -3.1135101<br>
0.5000 -7.9936657 0.0000000 236.27664 0.0000000 -1.1844406<br>
1.0000 -15.156097 0.0000000 204.58139 3.0517578e-05 -2.4874344<br>
<br>
<br>
Ignoring the floating point errors, we can see that 2018.1 and 2018.3 <br>
give more or less the same results, which are very different from those <br>
produced by 2018.4 and 2018.5, resulting in extremely large <br>
discrepancies in free energies - more than 20 kJ/mol (not shown here, <br>
but the other .xvg files exhibit the same behaviour). However, these <br>
discrepancies only seem to hold for the delta H values and not dH/dl. <br>
Finally, free energies calculated from 2019 using gmx bar seem to <br>
reproduce 2018.1 and 2018.3 but we can see that there is a missing <br>
column of data compared to other versions and most of the dH/dl <br>
derivatives do not agree with other versions of GROMACS. Note that this <br>
issue only seems to persist when perturbing the Coulomb interactions. <br>
Van der Waals perturbation energies seem consistent between versions <br>
(not shown here).<br>
<br>
<br>
Since the only variable for all of these simulations is the GROMACS <br>
version (which was compiled on the same computer with the same <br>
libraries), I highly suspect that there is (at least one) bug with the <br>
free energy implementation of the code (or the output thereof). However, <br>
I am not sure which version gives the "correct" results. Any feedback <br>
would be highly appreciated. I have not uploaded any files but if any <br>
more information is required, I am happy to provide it.<br>
<br>
<br>
Thank you very much.<br>
<br>
<br>
Kind regards,<br>
<br>
Miroslav<br>
<br>
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