[gmx-users] Calculating Long Ranged Coulomb and LJ for Groups in Simulation

Bukannan, Hussain Ameer M A hbukanna at tulane.edu
Fri Apr 26 08:27:57 CEST 2019


I am trying to calculate the interactions between a charged methane solvated in many water molecules. I have a -0.4 charge on the methane.

I used energygrps in the .mdp files but the only options that are showing are short ranged interactions. 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, espacially for the Coulombic interactions.

I also tried enemat but the it seems that it only gives me the average over all data points rather than the value at each timestep. The -nomean option seems to be not implemented yet.

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,

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