[gmx-users] Calculating Interactions Between Charged Methane and Water

Bukannan, Hussain Ameer M A hbukanna at tulane.edu
Sun Apr 28 07:38:26 CEST 2019

I am trying to calculate the interactions at each time point between a charged methane solvated in water molecules. I have a -0.4 artificial charge on the methane.

I used energygrps in the .mdp files but the only options that are showing when I use gmx energy are short ranged interactions for the groups.

I also tried using md -rerun with energygrp-excl to exclude the SOL-SOL interactions, however, it is requiring me to switch from using Velvet to group cutoff-scheme. When I do that I get results that are widely different than the ones with Velvet, especially for the Coulombic interactions.
I also tried using enemat but it is only giving me the averages rather than at each time point like gmx energy.

Is there another way to get the long ranged interactions (and the Coulomb reciprocal and
dispersion correlation) between only methane-SOL that lets me keep the Velvet cuttoff-scheme?

Thank you,

More information about the gromacs.org_gmx-users mailing list