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

Berk Hess hess at kth.se
Fri Feb 12 08:22:27 CET 2021


A TIP3P water molecule has no intramolecular interactions and a system 
of one water molecule therefore should have zero potential energy.
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.



On 2/12/21 7:00 AM, Igor Leontyev wrote:
> 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.
> Thanks,
> Igor

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