[gmx-users] pbc and tpr file

[tangxuan]

Hi, 
Thanks for your reply. The protein I simulated has 16 subunits. I
checked the protein struture (no jump) in the tpr file and there are no
contacts between each subunits. The protein structure in the fist frame
of simulation seems ok, but has jumps. Two strucutres are very different
and I do not why? Therefore,  something strange (rotation) will happen
to the system after I remove jumps in the trajectory.  Do you think it
is right to produce a new reference structure from the first frame by
tpbconv?


Thanks

Tang
On Wed, 2007-12-12 at 09:03 +0100, Tsjerk Wassenaar wrote:
> 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). 
> 
> Cheers,
> 
> Tsjerk
> 
> 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
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