[gmx-users] calculate *all* carbon atom distances over time?

Justin Lemkul jalemkul at vt.edu
Mon Feb 15 18:14:44 CET 2016

On 2/15/16 12:10 PM, Athina Meletiou wrote:
> Hello all,
> I was wondering how I could measure the distance over time between all my
> carbon atoms in my simulation. My molecules have interesting folding patterns
> and I would like to see the distances between the unconnected carbon atoms as
> my molecules fold and unfold through the simulation. My simulations consist
> of single lipid molecules in water.
> I have tried using g_dist but it seems that it's not what I'm looking for as
> it calculates distances between groups of atoms rather than individual atoms.

A "group" can be one atom.

> Do you think that gmx distance (Gromacs 5.0) will help me? What concerns me
> is that in the gmx distance reference it states that "gmx distance calculates
> distances between pairs of positions as a function of time" - do the
> positions need to be in pairs, as in always in even numbers?

If you're looking at distances between any two atoms, why would this be a concern?



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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