Hi Tsjerk, You have cleared my doubts. I had fitted the structures in the pdb files, which is why I was confused because different coordinates were encountered for the same time step in the original and extended run( that had crashed). Now I understand, where lies the problem.
Thank you very much. Sarbani On Thu, 11 Sep 2008 Tsjerk Wassenaar wrote : >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
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