Hello,<br><br>I am fairly new to using Gromacs and am writing to seek clarification on the g_rdf module.<br><br>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."<br><br>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 <i>outside</i> of (or around) the protein. The latter method produces RDF values within the protein (distance from its center-of-mass).<br>
<br>I ask this because I am unsure how to utilize the -com flag:<br><br>$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o rdf_protein.xvg (first method?)<br><br>$gromacs/g_rdf -f trajectory.xtc -n index.ndx -s protein.tpr -o rdf_protein.xvg -com (second method?)<br>
<br>Any helpful insights are most welcome.<br><br>Regards,<br>Lily<br>