Hi Sarbani, If you only want to extract coordinates from your trajectory it does not matter.
The trajectory file (.xtc) only contains coordinates. To make a pdb/gro/whatever file from it, you need to add information regarding atom/residue names, etc. That will be taken from a pdb/gro/tpr file, but will be the same for an initial or restart .tpr file. The pdb/gro/tpr file contains an atom list together with coordinates, and a .tpr file also contains topology information (masses, charges, bonds, angles, etc.). When using trjconv, this information may be used for fitting and for some pbc related operations. In that case it will matter which .tpr file you use for reference, since fitting against the initial set of coordinates will yield results different from a fit against coordinates from the end or midway a run. Options like -pbc nojump add further restrictions to the reference file you use, but for that do browse the archives, as I don't feel like elaborating on that again. Cheers, Tsjerk On Thu, Sep 11, 2008 at 8:12 AM, sarbani chattopadhyay <[EMAIL PROTECTED]> wrote: > Hi everyone, > I am facing a peculiar problem. > > > I had given an exteneded continuation run using the "tpbconv" command. > > The extended run had crashed due to power failure. I again gave an exact > continuation run > using the "tpbconv" command. > > After the run was over, I concatenated the trajectory files using "trjcat" > command. > > My question is that which ".tpr" file should I use when I use the "trjconv" > command to generate > the pdb file from the trajectory ie. should I use "extended.tpr" or > "restart.tpr ". > > Thanking You, > Sarbani > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
