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

[Marcelo Depólo]

Carlos,

You might want to try a PBC correction with -pbc nojump and another RDF
calculation with the corrected trajectory.

2014-09-19 19:10 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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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-- 
Marcelo Depólo Polêto
Biochemicist
University of Viçosa - Brazil