[gmx-users] nitrogen itp file with virtual site

Justin Lemkul jalemkul at vt.edu
Mon Jul 17 15:40:45 CEST 2017

On 7/16/17 9:20 PM, Ali Ahmed wrote:
> Hello GROMACS users,
> This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
> super critical point.The structure I use is different from regular nitrogen
> (N-N). As you know N atom has a negative charge which means the nitrogen
> molecule will be negatively charged, therefore I need to use massless and

This is incorrect - N2 carries no formal charge.

> charged virtual site to equilibrate the molecule. I have looked on the
> tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
> anyone have done it before tell me how to do it ?

You don't need virtual sites for a diatomic molecule.


> Here are the parameters:
> N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
> =(-0.482 e).
> XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge= 0.964
> e.
> Thank you very much.


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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