[gmx-users] Ion additon

Justin Lemkul jalemkul at vt.edu
Wed Jul 2 03:09:52 CEST 2014

On 7/1/14, 9:04 PM, Harshkumar Singh wrote:
> for some or the other reason I'm unable to install grace that is why I'm
> using Gnuplot.What is the conversion then? Is it the one mentioned on the
> website?

The format depends on the type of data, but none of that is really relevant 
here.  You can unformat any output (i.e. make it plain) with "-xvg none" with 
any Gromacs command.  Whatever other conversions are necessary depend on the 
software being used; consult its documentation.


> On Tue, Jul 1, 2014 at 7:12 PM, Harshkumar Singh <harshsingh2293 at gmail.com>
> 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?
>> Also how do I plot the xvg files using Gnuplot?
>> --
>> Harshkumar Singh
>> 2nd Year Integrated MSc Chemistry
>> IIT Bombay.


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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