You have a box with negligible dimensions, so as forecast above, your conversion process from AMBER was not as effective as it might have been. As you can see with g_rdf -h, it defaults to using periodic boundary conditions. You need to do something different.
Mark On Wed, Apr 10, 2013 at 2:38 PM, Venkat Reddy <venkat...@gmail.com> wrote: > Sir > > I truncated my file so it has only 10 molecules of water and 5 frames. > gmxcheck gives the following information > Checking file test.trr > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > # Atoms 30 > Last frame 5 time 0.500 > > > Item #frames Timestep (ps) > Step 6 0.1 > Time 6 0.1 > Lambda 6 0.1 > Coords 6 0.1 > Velocities 0 > Forces 0 > Box 6 0.1 > > And the output file for gmxdump is attached. They look fine in my limited > knowledge of gromacs that I have gained in the past couple of days. > > Please advice > > > On Tue, Apr 9, 2013 at 6:39 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > >> On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban <vvcha...@gmail.com> >> wrote: >> > So there is a problem with your trajectory file. Try to understand what >> > kind of problem it is. >> >> e.g. by using gmxcheck and/or gmxdump (on a small version of your >> data!) to see what information is present. >> >> Mark >> >> > >> > 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 >> > > > > -- > 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
