Hi Paul, I though you mean converting the .gro files to .xtc file using *trjcat *(which was my initial question), sorry about that. I see now, I just used *trjconv* to convert gro file them to .xtc files and then ... .
.gro ----trjconv----> .xtc ------trjcat----> .xtc(or trr) Thanks Alex On Mon, Oct 28, 2019 at 11:18 AM Paul bauer <paul.baue...@gmail.com> wrote: > Hello, > > I think I understood your problem (or at least hope so). > The issue is that it is no longer possible to directly concatenate text > based trajectory files, so I showed a possible way to work around the > problem. > You can also go back to a previous version of GROMACS to perform the > concatenation, but I can't promise you that it will work. > > Please let me know if you need extra help to get this to work. > > @Justin, here is the change that added the check for binary file > formats: c232242c29fb3ca63c8e1027eb70477069decdd9 > > Cheers > > Paul > > On 28/10/2019 15:42, Alex wrote: > > Hi, > > Paul, > > I guess you understood the question wrongly. I have some *.gro files and > I > > want to concatenate them to have a trr (or xtc) trajectory. > > > > Justin, > > Yes indeed, It would be great if gmx trjcat could concatenate the gro > files. > > > > Regards, > > Alex > > > > On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 10/28/19 6:26 AM, Paul bauer wrote: > >>> Hello, > >>> > >>> this looks like a case of misleading documentation. Can you file an > >>> issue for this please on redmine.gromacs.org? > >>> So that we don't forgot to fix this for the next patch release? > >>> A possible work around for you can be that you first convert your > >>> files to e.g. XTC format, use trjcat to combine them and convert them > >>> back to GRO. > >>> > >> Out of curiosity, why was this file format removed as an input for > >> trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB > >> files to make a psuedo-trajectory for ensemble analysis was rather > >> handy. Converting to an intermediate binary format is a workaround, but > >> why add the extra step? Did the trjcat code need de-complicating? > >> > >> -Justin > >> > >>> Cheers > >>> > >>> Paul > >>> > >>> > >>> On 27/10/2019 19:47, Alex wrote: > >>>> Any comment on this, please? > >>>> Thanks > >>>> ---------- Forwarded message --------- > >>>> From: Alex <alexanderwie...@gmail.com> > >>>> Date: Sat, Oct 26, 2019 at 9:38 AM > >>>> Subject: gmx trjcat > >>>> To: <gmx-us...@gromacs.org> > >>>> > >>>> > >>>> Dear all, > >>>> I want to concatenate some gro file to have a trr or xtc trajectory > file > >>>> out of them as gro files are also acceptable as input files, > >>>> according the > >>>> gmx trjcat man page; > >>>> > >>>> Options to specify input files: > >>>> -f [<.xtc/.trr/...> [...]] (traj.xtc) > >>>> Trajectory: xtc trr cpt *gro* g96 pdb tng > >>>> > >>>> So, I fed the .gro files in as input files likes; > >>>> gmx trjcat -f c*.gro -o trajout.trr > >>>> > >>>> However, I get below error that; > >>>> Fatal error: > >>>> gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) > >>>> > >>>> Any comment is highly appreciated. > >>>> Regards, > >>>> Alex > >>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > > -- > Paul Bauer, PhD > GROMACS Release Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
