I believe the problem is in the way which you used to convert AMBER trajectory to the GROMACS trajectory....
I would suggest to try gmxdump and see what your trajectory looks like. Oe maybe even better - try to visualize it in VMD to see if the format is correct. Dr. Vitaly Chaban Sir > > I was using an old version. Now I used 4.5.5, it still gives me the same > blank output file. > > Kindly suggest how to go about solving this > > Thanks > > > On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy <venkat...@gmail.com> > wrote: > > > > > There was no fatal error preceding the output. After selecting the > groups > > > following are the output on the screen > > > Reading frame 1 time 0.100 > > > Warning: can not make broken molecules whole without a run input file, > > > don't worry, mdrun doesn't write broken molecules > > > > > > > This message is from a prehistoric version of g_rdf. Please get a new > one. > > > > Mark > > > > > > > > > > Reading frame 2000 time 200.000 > > > > > > > > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman) > > > > > > And the rdf.xvg file looks like this > > > > > > #This file was created Sat Apr 6 10:54:13 2013 > > > # by the following command: > > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg > > > # > > > # g_rdf is part of G R O M A C S: > > > # > > > # GROningen MAchine for Chemical Simulation > > > # > > > @ title "Radial Distribution" > > > @ xaxis label "r" > > > @ yaxis label "" > > > @TYPE xy > > > @ subtitle "O21-H2_&_CAT" > > > 0.001 1 > > > ~ > > > > > > Whats going wrong? Please help. > -- 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
