[gmx-users] which "tpr" file to use

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Thu Sep 11 10:02:42 CEST 2008

  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.


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
>On Thu, Sep 11, 2008 at 8:12 AM, sarbani chattopadhyay
><sarbani_c84 at rediffmail.com> 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 at 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 gmx-users-request at gromacs.org.
> > 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080911/e062b6fa/attachment.html>

More information about the gromacs.org_gmx-users mailing list