Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg
Francesco 2013/4/16 Mark Abraham <mark.j.abra...@gmail.com> > On Apr 15, 2013 6:27 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > > > > On 4/15/13 12:23 PM, Steven Neumann wrote: > >> > >> Dear Gmx Users, > >> > >> I obtained dcd trajectory from simulation in another software. I wish to > >> merge many trajectories using trjcat with a proper timestep. Is that > option > >> possible using gromacs or shall use a script to produce tpr file from my > >> prmtop file e.g. amb2gmx ? Any links for such a script? > >> > > > > If you linked against VMD libraries when installing, Gromacs can handle > any trajectory/coordinate file format that VMD can, thus requiring no > conversion. If you need a .tpr file to do the analysis you are trying to > do, then yes, you need to convert topology information into the proper > format. > > ...and be aware that a -s option that accepts both .tpr and (say) .gro > formats (as shown in g_tool -h) might succeed with the latter if only atom > names, rather than (say) bonding connectivity is required for g_tool to > work. > > Mark > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://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 > -- > 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 > -- Cordiali saluti, Dr.Oteri Francesco -- 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