[gmx-users] gmx rdf

[Justin Lemkul]

On 6/20/16 9:22 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello gmx_users,
> I was trying to plot distribution function in a bilayer system using gmx
> rdf. I used the system as a reference ( thinking it will take the COM of
> the system as reference point) . Then I plotted RDF of a marked atom. But
> it is plotting only in the positive direction while the lipids in the
> lower leaflet are also containing the marked atom. So I am unable to see
> the distribution from center of the bilayer to the lower leaflet.
> Can anyone please help me out in identifying my mistake.
>

Distance is a positive value and that's what gmx rdf will always report.  If you 
want to distinguish between different leaflets, create an index file for the 
different leaflets; but gmx rdf will always report a positive number.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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