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

Justin Lemkul jalemkul at vt.edu
Mon Apr 13 14:39:24 CEST 2015

On 4/12/15 10:40 PM, atsutoshi.okabe at takeda.com wrote:
> Thank you for your help.
> Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these ligands.
> The reason why I add some ligand molecules(not one ligand) in simulation is to enhance ligand sampling.
> I tried using [distance_restaints] below, not use [bonds] because of domain decomposition error. Then, the MD simulation could run normally without domain decomposition error!
> [ distance_restraints ]
> ;ai aj type index type' low up1 up2 fac
> 13  63  1    1     1    20   100 100 10000
> However, the distance between 13 atom and 63 atom seems to be less than 20 angstrom in every steps of MD simulation.
> So I tried to change the fac value from 10000 to -10000, but the distance was less than 20 angstrom during MD simulation
> Why the ligands were restrained less than 20 angstrom although I think I add repulsive force between these atoms?

Depending on how structurally complex the ligands are, it may be very easy to 
define a dummy atom within the structure using a virtual site, then specifying a 
nonbonded interaction only between these virtual sites using [nonbond_params]. 
That way, these sites will not affect ligand-water, ligand-protein, etc but will 
repel ligands from one another.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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