>> Dear GROMACS people - >> >> I am calculating radial distribution function between the centers of >> mass of two large particles in a periodic box. >> >> My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f >> conf.gro >> >> My index file contains two groups of atoms standing for the first and >> the second supraparticles whose centers-of-mass I am interested in. >> Since here I provide the "conf.gro" file rather than a trajectory, I >> expect to get just one peak in my RDF, but instead I get multiple >> peaks at different separation distances (please, see >> http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index >> file are separated spatially, if this may matter. >> >> Would anyone kindly explain how the COM RDF function works? My >> ultimate purpose is to depict how the distance between those two >> centers-of-mass evolves in time. >> > > You also need to use the -com flag to use the COM of the reference group. > > -Justin >
The -com flag changed the output (please, see http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of embarassing peaks after 7nm. Given the positions of these supraparticles, I would expect maximum about 10nm whereas the box side is 26nm. >From the g_rdf help message -- The option -rdf sets the type of RDF to be computed. Default is for atoms or particles, but one can also select center of mass or geometry of molecules or residues. In all cases, only the atoms in the index groups are taken into account. I understand this in the following way. The centers-of-mass of the groups in the index file are computed and further the calculation proceeds as if these COMs were regular atoms. If I have only two groups, I should get one maximum. Am I not correct? Vitaly -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
