30 mar 2007 kl. 12.40 skrev Marc Baaden:
Dear All,
for convenience I wanted to re-orient a simulation system that's
currently running fine by applying a rotation of 270 deg around
the y axis (using editconf -rotate 0 270 0). In the corresponding
gro file I thus exchanged the x and z box dimensions to get the
right periodicity, going from
17.34860 17.79878 12.71904 0.00000 0.00000 0.15222
0.00000 0.27635 -0.00236
to
12.71904 17.79878 17.34860 0.00000 0.00000 0.15222
0.00000 0.27635 -0.00236
But apparently I missed out on something, as the rotated simulation
box crashes immediately in an MD.
I wonder whether this could have something to do with the other 6
parameters
on the line, but I don't quite know what they are and how they need
to be
adapted with respect to the rotation that I have applied.
Have a look at the description of the gro-format. You can find it on
the website. All nine numbers are the x-, y- and z components of the
box vectors.
Any help would be appreciated,
thanks in advance,
Marc Baaden
NB: is there is a tool for doing a rotation and updating the
periodic cell
information accordingly?
--
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
Postdoc in Computational Biology available:
http://www.shaman.ibpc.fr/fonflon_postdoc.pdf
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Laboratory of Molecular Biophysics,
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