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<div class="moz-cite-prefix">Are you running on CPU or GPU?<br>
<br>
/Berk<br>
<br>
On 2021-02-12 12:23 , Igor Leontyev wrote:<br>
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Sorry, for the confusion. I meant of course group-rest terms.<br>
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Assuming my energy group includes 1 TIP3P molecule and has name
WAT1.</div>
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I got zeroes when I extract energy for terms:</div>
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Coul-SR:WAT1-rest</div>
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LJ-SR:WAT1-rest</div>
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but they should include non-zero interaction with all neighbors
within the Cutoff.<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Igor
Leontyev <a class="moz-txt-link-rfc2396E" href="mailto:ileontyev@ucdavis.edu"><ileontyev@ucdavis.edu></a><br>
<b>Sent:</b> Friday, February 12, 2021 2:09 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" 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>Subject:</b> Re: Zero short-range energy of TIP3P</font>
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Thanks, Berk, for the response. I understand that a single
water molecule in the vacuum box should have no Short-Range
energy. But I am talking about water molecule in the BULK,
i.e. there are a lot of explicit H2O around. I expect that SR
energy (with PME electrostatics) includes at least LJ
interactions with all neighbors within the CutOff, and may be
also Coul interactions (not sure how PME splits the energy
into SR and LR). But I get exact zeroes for both LJ and Coul
terms.</div>
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Igor<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Igor
Leontyev<br>
<b>Sent:</b> Thursday, February 11, 2021 10:00 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" 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>Subject:</b> Zero short-range energy of TIP3P</font>
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Dear gmx developers,
<div>The short range energy terms (Coul and VdW) for a
single water molecule in the bulk (rigid TIP3P) simulated
with gmx-2020 and extracted from edr-file are exact zero.
The result looks strange to me. The same but with gmx-5.1
gives non-zero (presumably correct) interaction energy of
water.</div>
<div><br>
</div>
<div>How I do it:</div>
<div>1. Generate an index file with indices of the specific
water molecule in the bulk (e.g. for the 1st H2O it is
just 1 2 3) to be monitored.</div>
<div>2. Specify the energy group of the molecule to be
monitored in mdp file and run MD.</div>
<div>3. After MD, use gmx energy to get LJ and Coulomb (SR)
interactions of the energy group from the edr file.</div>
<div>The computed with gmx-2020 non-bonded (SR) energies of
this energy group are zero.</div>
<div><br>
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<div>Please, let me know if I am doing something wrong.
Otherwise, it looks like a bug because old version
(gmx-5.1) results in non-zero energies that looks
reasonable.</div>
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<div>Thanks,</div>
Igor<br>
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