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
