[gmx-users] User Defined Potentials

Justin Lemkul jalemkul at vt.edu
Tue Apr 25 14:47:27 CEST 2017

On 4/24/17 5:58 PM, Ommair Ishaque wrote:
> Hi,
> I am Phd physics phd student at University of Delaware. I am using GROMACS
> for calculation of solvation energy of argon or methane in water. But Our
> water model has additional interaction terms other than already define in
> GROMACS. *Can we add our own interaction terms in GROMACS? If yes how?*

GROMACS allows the use of tabulated potentials so you can apply whatever 
functional form you like without having to mess with the source code.

> And one of my senior colleagues was telling me in past, GROMACS had no
> quaternion algorithm for rigid molecules. It handles rigid molecules using
> SHAKE/RATTLE/LINCS. If this is still the case, I am not entirely sure how
> we will be able to use it for our water model (CC-5spol) which has at least
> 25 sites. *If there is now a means of truly propagating the motion of rigid
> molecules without SHAKE/RATTLE/LINCS, this will be great.*

SHAKE, SETTLE, and LINCS are your only options in GROMACS for rigid molecules.



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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