[gmx-users] Simulation cell rotation and CRYST1/periodic box information

Marc Baaden baaden at smplinux.de
Fri Mar 30 12:40:00 CEST 2007

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


  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.

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:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

 Postdoc in Computational Biology available:

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