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

[Carlos Navarro Retamal]

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?
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.
 Best regards,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl


On Friday, September 19, 2014 at 6:48 PM, Justin Lemkul wrote:

>  
>  
> On 9/19/14 5:39 PM, Carlos Navarro Retamal wrote:
> > Not at all. I’m using the .xtc file that comes from the simulation.
> > What do you mean with the nrexcl issue? Is there a way i can fix it?
> >  
>  
>  
> The g_rdf help text describes issues related to nrexcl, but probably it's  
> unrelated. I suspect you're probably getting issues related to periodicity,  
> since the COM of a protein "broken" across a box is coincident with the box  
> center, where you also have solvent. Remove periodicity and/or center the  
> protein in the box and re-run g_rdf.
>  
> -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 (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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