See style 8 for trjconv -h Mark
On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri <francesco.ot...@gmail.com > wrote: > 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 > -- 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