Dear Gromacs users, I tried g_rdf function and have obtained a strange result: usually the RDF curve looks like relaxing oscillations around 1.0 constant level, but in my case it appears to be oscillation around exponent going from 0.0 at zero distance to 1.0 at large distances.
Is the RDF obtained correct? I used the command as follows: g_rdf -f MT.trr -s MT.tpr -n rs.ndx -o MT.RD.xvg -bin 0.05 -pbc -rdf res_cog where file MT.trr contains ~150 ps of equilibrated trajectory of 582 residue protein in water; The "reference group" was chosen "Water" and the "1 group" was taken from index file rs.ndx. The latter group contains two tip NHH groups of charged arginine. (This residue was inspected on exposing to solvent and showed one of the largest solvent accessible surface). Thanks in advance, Igor Shchechkin -- View this message in context: http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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