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

[Carlos Navarro Retamal]

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?
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 or 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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