[gmx-users] How to add a repulsive harmonic potential

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 14 11:27:52 CET 2014


You can use a distance restraint (see manual) implemented with [bonds] type
10. In current released code, the atoms need to be within the same
[moleculetype], which would likely mean you need to aggregate the ligands'
topology definitions so that you can refer to atoms in different actual
molecules that are now within the same [moleculetype] Alternatively, there
is draft code for inter-molecular bonded interactions at
https://gerrit.gromacs.org/#/c/2566/, but nobody has yet tried that it


On Fri, Nov 14, 2014 at 10:45 AM, <atsutoshi.okabe at takeda.com> wrote:

> Dear all
> To avoid ligand aggregation under higher concentration, I would like to
> introduce a weak repulsive potential term between the specific(e.g
> nitrogen) atoms of ligand molecules in the Protein/Ligand/Water system.
> This potential set as below.
> U(R) = K(R-R0)^2, if R<R0 (repulsive potential)
> U(R) = 0, if R>R0
> Could you tell me how to add the repulsive harmonic potential in MD
> simulation?
> Bests,
> Atsutoshi Okabe
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