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<div class="moz-cite-prefix">Hi,<br>
<br>
A TIP3P water molecule has no intramolecular interactions and a
system of one water molecule therefore should have zero potential
energy.<br>
You don't write what Coulomb interaction type you are using. With
reaction-field, a single water molecule has an interaction with
the dielectric medium beyond the cut-off. This interaction used to
be accounted for in the SR term, but is now in the LR term. For
PME the SR term used to contain the correction for excluded pairs
of the grid interaction, but this has been moved some time ago to
LR.<br>
<br>
Cheers,<br>
<br>
Berk <br>
<br>
On 2/12/21 7:00 AM, Igor Leontyev wrote:<br>
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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>
<br>
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