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<div class="moz-cite-prefix">Hi,<br>
<br>
Maybe I don't understand what you mean. Your instructions are
incorrect. You said "select the energy group". But for non-bonded
interactions there are only energy group pairs. If you pairs is
molecule 1 vs molecule 1, that should have zero LJ SR and Coulomb
SR energy in 2020.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2/12/21 11:09 AM, Igor Leontyev wrote:<br>
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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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<br>
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Igor<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<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>
</div>
<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>
<div><br>
</div>
<div>Thanks,</div>
Igor<br>
</div>
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