rainy...@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
--
========================================
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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