On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy <[email protected]> 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 <[email protected]> wrote: > > > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy <[email protected]> > 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 [email protected] > > 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 [email protected]. > > * 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
