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

[Carlos Navarro Retamal]

Hi Marcelo,
Thanks for your reply.
Sadly it didn’t work either, so i’m trying to generate a new .tpr file by changing the nrexcl values just as Justin suggest.
Hope this may works.
Thanks the two of you.
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 8:58 PM, Marcelo Depólo wrote:

> 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 (mailto: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 (mailto: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
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