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 <[EMAIL PROTECTED]> wrote:
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] 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
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