[gmx-users] Question regarding g_rdf

[Justin A. Lemkul]

rainy908 at yahoo.com wrote:
> Hello,
> 
> I am fairly new to using Gromacs and am writing to seek clarification on 
> the g_rdf module.
> 
> In the manual, it states that "g_rdf calculates radial distribution 
> functions in different ways. The normal method is around a (set of) 
> particle(s), the other method is around the center of mass of a set of 
> particles."
> 
> Suppose a protein is solvated in a cubic water box.  If I interpret this 
> correctly, the former method only produces RDF values at a distance 
> /outside/ of (or around) the protein.  The latter method produces RDF 
> values within the protein (distance from its center-of-mass).
> 

Your interpretation is incorrect.  A normal RDF plots probabilities of distances 
between any atom pairs in the given index groups.  Invoking the -com flag simply 
means that the center of mass of the protein, not all of its constituent atoms 
individually, is used as the reference in the RDF plot.

-Justin

> I ask this because I am unsure how to utilize the -com flag:
> 
> $gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o 
> rdf_protein.xvg  (first method?)
> 
> $gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o 
> rdf_protein.xvg -com  (second method?)
> 
> Any helpful insights are most welcome.
> 
> Regards,
> Lily
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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