Thank you sir for the valuable input. I will look into the matter and get to you.
On Thu, Apr 11, 2013 at 2:40 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 >> > > -- 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
