[gmx-developers] Zero short-range energy of TIP3P

Igor Leontyev ileontyev at ucdavis.edu
Fri Feb 12 11:09:23 CET 2021

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.

From: Igor Leontyev
Sent: Thursday, February 11, 2021 10:00 PM
To: gmx-developers at gromacs.org <gmx-developers at gromacs.org>
Subject: Zero short-range energy of TIP3P

Dear gmx developers,
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.

How I do it:
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.
2. Specify the energy group of the molecule to be monitored in mdp file and run MD.
3. After MD, use gmx energy to get LJ and Coulomb (SR) interactions of the energy group from the edr file.
The computed with gmx-2020 non-bonded (SR) energies of this energy group are zero.

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.

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