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

[Erik Marklund]

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: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:
>  http://www.shaman.ibpc.fr/fonflon_postdoc.pdf
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys