Re: [gmx-users] Re: RDF output has no data
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 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 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 time0.000 >> # Atoms 30 >> Last frame 5 time0.500 >> >> >> Item#frames Timestep (ps) >> Step 60.1 >> Time 60.1 >> Lambda 60.1 >> Coords 60.1 >> Velocities 0 >> Forces 0 >> Box 60.1 >> >> 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 wrote: >> >>> On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban >>> 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 >>> 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 >>> 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 time0.100 >>> > > > > 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 frame2000 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 "" >>> >
Re: [gmx-users] Re: RDF output has no data
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 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 time0.000 > # Atoms 30 > Last frame 5 time0.500 > > > Item#frames Timestep (ps) > Step 60.1 > Time 60.1 > Lambda 60.1 > Coords 60.1 > Velocities 0 > Forces 0 > Box 60.1 > > 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 wrote: > >> On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban >> 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 >> 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 > >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 >> 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 time0.100 >> > > > > 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 frame2000 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 listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search th
Re: [gmx-users] Re: RDF output has no data
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 time0.000 # Atoms 30 Last frame 5 time0.500 Item#frames Timestep (ps) Step 60.1 Time 60.1 Lambda 60.1 Coords 60.1 Velocities 0 Forces 0 Box 60.1 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 wrote: > On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban > 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 > 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 >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 > 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 >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 time0.100 > > > > > 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 frame2000 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 listgmx-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-600
Re: [gmx-users] Re: RDF output has no data
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban 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 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 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 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 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 > > wrote: > > > > > > > There was no fatal error preceding the output. After selecting the > > groups > > > > following are the output on the screen > > > > Reading frame 1 time0.100 > > > > 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 frame2000 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Re: RDF output has no data
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 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 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 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 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 > wrote: > > > > > There was no fatal error preceding the output. After selecting the > groups > > > following are the output on the screen > > > Reading frame 1 time0.100 > > > 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 frame2000 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 listgmx-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 listgmx-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
Re: [gmx-users] Re: RDF output has no data
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 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 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 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 >> > >wrote: >>> > >>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy >>> > wrote: >>> > > >>> > > > There was no fatal error preceding the output. After selecting the >>> > groups >>> > > > following are the output on the screen >>> > > > Reading frame 1 time0.100 >>> > > > 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 frame2000 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 listgmx-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 listgmx-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
Re: [gmx-users] Re: RDF output has no data
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 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 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 > > >wrote: >> > >> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy >> > wrote: >> > > >> > > > There was no fatal error preceding the output. After selecting the >> > groups >> > > > following are the output on the screen >> > > > Reading frame 1 time0.100 >> > > > 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 frame2000 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 listgmx-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 listgmx-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
Re: [gmx-users] Re: RDF output has no data
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 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 > >wrote: > > > > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy > > wrote: > > > > > > > There was no fatal error preceding the output. After selecting the > > groups > > > > following are the output on the screen > > > > Reading frame 1 time0.100 > > > > 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 frame2000 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 listgmx-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 listgmx-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
