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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 11 08:49:48 CEST 2008

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
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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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