[gmx-users] RDF

Justin Lemkul jalemkul at vt.edu
Tue May 19 13:34:55 CEST 2015

On 5/19/15 4:12 AM, mah maz wrote:
> Thanks Justin! I cant find so much details in the manual; there are only
> general facts. does g_density give partial density?

Read the first sentence of the help description :)


> On Mon, May 18, 2015 at 11:25 AM, mah maz <mahmaz71 at gmail.com> wrote:
>> Hi Justin
>> The fact is I want to calculate water density in the system. If I select
>> group1: oxygen and group2: oxygen, g_rdf command gives me very large
>> numbers. Is it the number of atoms that should be changed to g/cm3?
>> Besides, what does it calculate, each O is a reference atom during
>> calculation?
>> Thanks a lot!
>> On Sun, May 17, 2015 at 2:17 PM, mah maz <mahmaz71 at gmail.com> wrote:
>>> Dear all,
>>> I want to calculate the radial distribution function of water molecules
>>> in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers
>>> which is not logical I suppose. Is it meaningful if I separate oxygen and
>>> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
>>> reference atom necessary to get RDF?
>>> Thanks!


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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