[gmx-users] pair distribution function

Justin Lemkul jalemkul at vt.edu
Sun Oct 6 16:42:02 CEST 2013

On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
> I have simulations for different peptides in POPC bilayer.
> I want to calculate pair distribution function (pdf) between negatively
> charged phosphate residue of POPC and positively charged residues of
> peptide. Is there any tool available in gromacs for plotting these values?

The closest you can get with a built-in Gromacs program is a radial distribution 
function with g_rdf.

> Secondly, how to calculate the center of mass for a bilayer?

g_traj -ox -com



Justin A. Lemkul, Ph.D.
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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