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<p>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.</p>
<p>Miroslav<br>
</p>
<div class="moz-cite-prefix">On 29/01/2019 21:38, Michael R Shirts wrote:<br>
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<p class="MsoNormal">I am happy to take a look, but please submit an issue (with exactly this information) and upload the files you used!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="color:black">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">~~~~~~~~~~~~~~~~<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Michael Shirts<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Associate Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="mailto:michael.shirts@colorado.edu" moz-do-not-send="true"><span style="color:#0563C1">michael.shirts@colorado.edu</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.colorado.edu%2Flab%2Fshirtsgroup%2F&data=01%7C01%7CM.Suruzhon%40soton.ac.uk%7Ca64f5f16ee4f452d537308d6863228a0%7C4a5378f929f44d3ebe89669d03ada9d8%7C1&sdata=CrU7hWN%2Ba0dy0fzSGbDKV0p6HWg0IGx7uZHlCW5Zorw%3D&reserved=0" originalsrc="http://www.colorado.edu/lab/shirtsgroup/" shash="I4yki7D5YfJDXXiM67ks2on/0GGXvI9hTI6CRR17B6AUO5SL7iq/GshEiSWsVc6Gi8L2WWSUqVCBWHYAz3IZ0q2Vk31uPimnG65LNaLDuHR9m6hHdPVgiofZtRDCD9+Dg7rAZkJLlXxYm82daCA32tX3VbTpz9tpEReA7NoBy0Q=" moz-do-not-send="true"><span style="color:#0563C1">http://www.colorado.edu/lab/shirtsgroup/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Phone: (303) 735-7860<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Office: JSCBB C123<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"><gromacs.org_gmx-developers-bounces@maillist.sys.kth.se></a>
on behalf of Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:mark.j.abraham@gmail.com">
<mark.j.abraham@gmail.com></a><br>
<b>Reply-To: </b><a class="moz-txt-link-rfc2396E" href="mailto:gmx-developers@gromacs.org">"gmx-developers@gromacs.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-developers@gromacs.org"><gmx-developers@gromacs.org></a><br>
<b>Date: </b>Tuesday, January 29, 2019 at 10:38 AM<br>
<b>To: </b><a class="moz-txt-link-rfc2396E" href="mailto:gmx-developers@gromacs.org">"gmx-developers@gromacs.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-developers@gromacs.org"><gmx-developers@gromacs.org></a><br>
<b>Cc: </b><a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">"gromacs.org_gmx-developers@maillist.sys.kth.se"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">
<gromacs.org_gmx-developers@maillist.sys.kth.se></a><br>
<b>Subject: </b>Re: [gmx-developers] XVG Energy Discrepancies Between GROMACS Versions<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Thanks for the report! There was at least one relevant bug fix in 2018.4 - see <a href="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" originalsrc="http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html" shash="RWJUMk/TXgEvdhy+ihnyPpXqHUUE81rjy+cmlakcHrVeA4Azc43LovJmNacd+qIQ8xEsQKfEie/D9QyrT2BIWSaseUsMa8zQIv0DSGcsufJ29e81a0DoLPx7t52ZzZV+zzf186w20gKfKgsEf6PfmOz4YAgceboxBN2dQ6qLZvk=" moz-do-not-send="true">http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html</a>.
But doubtless there is more to investigate here.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Mark<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Jan 29, 2019 at 5:46 PM Miroslav Suruzhon <<a href="mailto:ms2m18@soton.ac.uk" moz-do-not-send="true">ms2m18@soton.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">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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