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 -- 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
