<div dir="ltr">Hi Vytas,<div><br></div><div>If you expect it's a problem, upload specific files to redmine (not just a TPR, but complete input) where results ideally differ after just 1-5 steps, and describe what you expect vs. what you get!</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 27, 2020 at 2:46 PM Vytautas Gapsys <<a href="mailto:vgapsys@gwdg.de">vgapsys@gwdg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hey,<br>
<br>
I have encountered an unexpected outcome when calculating solvation free <br>
energies and using the option: couple-intramol = no<br>
<br>
The observation is that the forces, overall electrostatic energy and the <br>
final free energy depend on the rcoulomb cutoff, in spite of using PME.<br>
<br>
I speculate that the following might be happening: for this simulation, <br>
intramolecular interactions are replaced by explicit pair interactions, <br>
however, this apparently is done for both states - coupled and <br>
decoupled. This way, in the coupled state those intramolecular <br>
electrostatic interactions that are outside of the rcoulomb cutoff are <br>
counted twice (when using PME): once they are counted explicitly <br>
ignoring the rcoulomb cutoff, second time they appear in the reciprocal <br>
part of PME.<br>
<br>
This can be verified by extending rcoulomb up to the point where all the <br>
intramolecular interactions are within the rcoulomb cutoff. When <br>
extending the cutoff further from that point the overall electrostatic <br>
energy becomes rcoulomb independent.<br>
<br>
Such a dependence on rcoulomb is problematic, as tunepme can change <br>
rcoulomb value during runtime.<br>
<br>
Let me know if I am overlooking something and maybe this behaviour can <br>
be circumvented.<br>
<br>
Best Regards,<br>
Vytas<br>
<br>
-- <br>
Vytautas Gapsys<br>
Project Leader at Max Planck Institute for Biophysical Chemistry<br>
Computational biomolecular dynamics group<br>
Am Fassberg 11<br>
D-37077 Goettingen, Germany<br>
Email: vgapsys[at]<a href="http://gwdg.de" rel="noreferrer" target="_blank">gwdg.de</a><br>
Phone: +49 551 201-2310<br>
<br>
-- <br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>></div><div>Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University</div><div>Science for Life Laboratory, Box 1031, 17121 Solna, Sweden</div></div></div></div></div></div></div></div></div>