[gmx-users] Problem with trjconv centering after fitting

[Tsjerk Wassenaar]

Hi,

Would that be the same? What happened here is that the system was
first fitted. Thus, the system is rotated and any operation concerning
pbc after that point will be screwed up, because the box definition
does not match the system. Solution: first perform all operations
involving pbc, then fit the system. Note that translations are not a
problem, only rotations. An alternative solution would be to have all
routines involving rotation of the frame also rotating the box
definition in that frame in the trajectory. But this requires
modifications in many routines.

Tsjerk

On 8/28/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> chris.neale at utoronto.ca wrote:
> > Starting from a rhombic dodecahedron xtc file,
> >
> > trjconv -fit rot+trans -f a.xtc -s a.tpr -o a_fit.xtc
> > trjconv -center rect -pbc whole -f a_fit.xtc -s a.tpr -o a_fit_cent.xtc
> >
> > Visualization of a.xtc and a_fit.xtc via VMD are as expected. Nevertheless,
> > a_fit_cent.xtc shows overlapping atoms and regions of zero density. Why is this?
> >
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> could this be the same problem as reported here:
>
> http://bugzilla.gromacs.org/show_bug.cgi?id=99
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336