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). 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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