> 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?
No. It is not 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 > Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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
