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. > > > > > > On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy <venkat...@gmail.com> > > wrote: > > > > > > > Dear users > > > > > > > > I have used AMBER MD package to run simulation for a solvent box. I > am > > > now > > > > using the gromacs utility to calculate rdf as follows: > > > > > > > > g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg > > > > > > > > However, I get no data in the output rdf.xvg. Since Im using > specially > > > > generated force field parameters, I do not know how to go about > > > generating > > > > a tpr file (in case that is the problem). The rdf.ndx file is correct > > for > > > > my atom selection. Please suggest how to go about solving this. > > > > > > > > > > > Blank output usually indicates the command failed, which should have > been > > > preceded by a rather obvious fatal error. If a .tpr file is required, > > g_rdf > > > will tell you (again, a fatal error). > > > > > > -Justin > > > > > > -- > > > > > > ======================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) > > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- > > > 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 > > > -- > 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