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

[Carlos Navarro Retamal]

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?


--  
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 6:21 PM, Justin Lemkul wrote:

>  
>  
> On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote:
> > I Justin,
> > Thanks for your reply.
> > Sadly, that’s not the only bizarre peak,as you can see on the next image:
> > http://cl.ly/1B3B2y3I0o1R
> > This is how it looks when i don’t consideren the COM as a reference:
> > http://cl.ly/3m0d2W2y0N1Y
> > What; i your opinion, could be the problem?
> >  
>  
>  
> No idea, aside from the nrexcl issue I mentioned before. I don't know exactly  
> why that would be a problem, but that's all I could suggest. Has the trajectory  
> been manipulated in any way, e.g. with trjconv?
>  
> -Justin
>  
> > I think i’ll just have to use the second image to show the RDF.
> > Thanks a lot for your valuable help,
> > 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 (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> >  
> >  
> > On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:
> >  
> > >  
> > >  
> > > On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
> > > > Hi Justin,
> > > > First of all thanks for your reply.
> > > > It worked, but i’m getting weird results.
> > > > When i measured the RDF between:
> > > > Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm, which doesn’t make any sense (because i presumed that at this distance there must be a steric effect) am i right? Because this is my first time considering the center of mass of a molecule, so i don’t really know which distances are ‘normal’ are which are not considering one group as a COM of the protein.
> > > >  
> > > > i used the next command:
> > > >  
> > > > > g_rdf -f npt_production.xtc -com -s npt_production.tpr-o TEST-glycerol.xvg
> > > >  
> > > > group 1: Protein
> > > > group 2: GOL (glycerol molecules)
> > > >  
> > >  
> > >  
> > >  
> > > Indeed a distance of 0.022 nm would be physically impossible (that's 1/5 the
> > > length of a C-H bond!), so it's something else. I wouldn't expect it to be an
> > > issue, but note that g_rdf warns about the value of nrexcl in the topology.
> > > Probably some intramolecular terms are contributing in a weird way. If this is
> > > the only bizarre peak, you can probably safely ignore it using g_rdf -cut 0.05
> > > or something similar.
> > >  
> > > -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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> --  
> ==================================================
>  
> 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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