So there is a problem with your trajectory file. Try to understand what kind of problem it is.
I can recollect that I experienced something like that why translating CPMD trajectory to GROMACS. Maybe, it does not write time for each frame at the right place -- just a guess. Dr. Vitaly Chaban On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy <venkat...@gmail.com> wrote: > Sir > > I tried g_msd, after asking for group selection the program appears not to > read the frames as it remains stuck at reading frame 0, time 0.00. > > What to do? > > Thanks > > > > > On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > >> 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 >>> >> >> > > > -- > 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
