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