[gmx-users] User defined potentials with implicit solvent

Justin Lemkul jalemkul at vt.edu
Tue Mar 7 18:55:33 CET 2017

On 3/7/17 10:12 AM, John Stoppelman wrote:
> Hello all,
> I am currently testing an oligomer using implicit solvent. The system I am
> looking at was developed with custom parameters that were added to the
> CHARMM forcefield in GROMACS. I am attempting to increase the vdw
> interactions between the Carbon atoms in the backbone of the molecule,
> because I have reason to believe that these are too weak. I was trying to do
> so by following the instructions in this file:
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf However, I have
> realized that user defined potentials are not allowed in implicit solvent.
> Does anyone know of any way for me to accomplish the same purpose of
> increasing the interactions between select atoms in the implicit solvent
> model?

Increasing LJ attraction between atoms is typically done via NBFIX in CHARMM (a 
[nonbond_params] directive in GROMACS) to override combination rules.  This is 
fully supported as it does not require modification of the functional form.



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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