[gmx-users] Ion additon

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 01:16:26 CEST 2014

On 7/1/14, 7:12 PM, Harshkumar Singh wrote:
> I have used the genion option to add Mg2+ ion using the OPLS force
> field.When I open the .gro file in VMD I really cannot see the ion but the
> Mg ion is mentioned in the .gro file.Is this addition correct?

If it's in the .gro file, it's there.  Render as VDW/sphere and you will see it.

> Also how do I plot the xvg files using Gnuplot?

You don't.  The two programs require different formats, but conversion is fairly 



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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