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

[Carlos Navarro Retamal]

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)



Thanks again 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 Thursday, September 18, 2014 at 4:10 PM, Justin Lemkul wrote:

>  
>  
> On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
> >  
> > Dear gromacs users,
> > In order to measure the interactions between a Protein with respect to a mixture solvent solution (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol respectively.
> > By now i have measured g(r) between:
> >  
> > Protein - Glycerol
> > Protein Backbone - Glycerol
> > SideChain - Glycerol
> >  
> > but sadly, because i’m considering a huge amount of atoms of the Protein, the RDF graphic doesn’t look that good.
> > On that way i thought that maybe a better approximation will be to measure the RDF between the center of Mass of the protein with respect to the glycerol molecules, but i don’t know how to use make_ndx to create such kind of group.
> >  
>  
>  
> It's not a task for make_ndx. g_rdf does this with the -com option.
>  
> -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.
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>  
> jalemkul at outerbanks.umaryland.edu (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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