Do you experience this problem with g_rdf only, or with all gromacs analysis utilities?
On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy <venkat...@gmail.com> wrote: > Sir > > I loaded the trajectory. There doesn't seem to be anything wrong with it. > Have no clue whats going wrong > > Thanks > > > On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > >> 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 >> > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- 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