Dear Justin and Dash, Thank you for the kind response. I have another related problem. My xtc file is huge ~ 15 GB as I ran my calculation for 5 ns in a big box. I can convert the .xtc to .gro but I would like to do it in parallel using the cluster as it ran for a long time when I used the head node. However, when I use the below syntax and submit the job to the queue it is asking for a group index that I do not know how to provide when using the cluster to run the job.
gmx_mpi trjconv -s *.tpr -f *.xtc -o conf.gro -sep In this case, what should I do please? *Thank you* *Gangotri * On Mon, Sep 18, 2017 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/18/17 4:18 PM, gangotri dey wrote: > >> Hello! >> >> I would save it in vmd all at once but I would like to ideally save it in >> separate files. Also, the trajconv statement did not work. >> >> > Your original error will be solved by passing a .tpr file to trjconv -s, > as suggested below. If you want to save intervals of time into separate > files, use -b and -e. > > -Justin > > >> *Thank you* >> >> *Gangotri * >> >> >> >> >> >> On Mon, Sep 18, 2017 at 3:08 PM, R C Dash <rcdash0...@gmail.com> wrote: >> >> Open you the gro file in VMD. Add load data and show the trr or xtc file. >>> right click on to it and save coordinate. File type. gro. >>> or >>> trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro >>> >>> RC Dash, >>> >>> >>> On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey <holyriv...@gmail.com> >>> wrote: >>> >>> Dear all, >>>> >>>> I would like to transform my trajectory file n.trr or n.xtc to n.gro >>>> after >>>> my production run. I have used trjcat and trjconv to transform it using >>>> the >>>> index file. But in both the cases, it says "Can not write a gro file >>>> without atom names". How can I transform it please? >>>> >>>> >>>> >>>> *Thank you* >>>> >>>> *Gangotri * >>>> -- >>>> 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. >>>> >>>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > > -- > 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.