[gmx-users] RDF analysis with respect to center of mass of otein

[Justin Lemkul]

On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:
> Hi Justin,
> Thanks again for all your help.
> If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results?

A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect 
the outcome.

> In any case i centered the protein with the following command:
>
>
>> trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o traj_center.xtc
>>
>>
>>
>
> and then i measure the RDF with the following one:
>> g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o TEST-carbons.xvg
>
> But i’m still seeing these weirds peaks a short distance.

Unlikely, but it could be related to nrexcl; that's what you should try next.

-Justin

-- 
==================================================

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

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