[gmx-users] pbc and tpr file

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Dec 12 09:03:33 CET 2007

Hi Tang,

It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file
contains the protein "in one piece", if you want to use it as a reference
structure for rmsd calculations. You can extract the coordinates from the
.tpr file using editconf and then have a look. Actually, you should've done
this prior to removing jumps from the trajectory, since you must be sure to
remove the jumps in the right way (check the archives for more discussion on
these issues).



On Dec 12, 2007 1:42 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> tangxuan wrote:
> > hi all,
> >  I want to calculate the rmsd of my protein. If I remove the jump in the
> > xtc file or trr file, what should I do with tpr file?
> Nothing. Depending on your inputs to g_rms, it might provide your
> reference structure.
> Mark
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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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