[gmx-users] Turning off electrostatic interactions between two proteins

Ozlem Ulucan ozlem.ulucan.acan at gmail.com
Thu Oct 16 15:37:24 CEST 2014

Dear Gromacs users,

I am performing MD simulations of protein protein association. I would like
to turn off the electrostatic  interactions between my protein partners
while keeping the full interactions between each protein and the solvent.

At first I thought about using 1) free energy code, 2) energygrp-excl
option in MDP file or 3) coulombtype = PME-User

1) I guess one cannot decouple a particular molecule from another molecule
while keeping the interactions with solvent unchanged. Is this possible
using free energy code?

2) Using the energygrp-excl option will exclude all interactions. However,
I would like to keep at least the repulsive LJ part to avoid overlaps.

3) Setting  coulombtype = PME-User option and using user tables, I can only
turn off the electrostatic interactions up to the cut off value. The rest
of the proteins will still interact. If I use coulombtype = User, the
protein-solvent interactions will not be calculated beyond the cutoff.

Any suggestion will be highly appreciated.


More information about the gromacs.org_gmx-users mailing list