[gmx-developers] Heads up! trjconv broken

[Anton Feenstra]

On 15/06/10 10:34, Tsjerk Wassenaar wrote:
> Hi,
>
>> Do the trajectory formats allow the storage of rotated boxes? In that case
>> any operation that rotates the coordinates should also rotate the box. (But
>> then the PBC routines should also work with arbitrary rotated boxes!)
>
> Of course. The box is saved as a 3x3 matrix, which allows specifying
> any lattice in 3D. The only thing is that quite a number of routines
> need to be updated. E.g., the main fitting routine (do_fit) needs to
> get the box matrix as argument, and all calls to it need to pass the
> box (or a dummy box).
> But doing so makes the resulting boxes non-compliant with Gromacs
> rules, making calls to PBC routines break. That means that all PBC
> operations need to be modified too. One way would be to pretransform
> box and coordinates back to easy to handle orientation prior to PBC
> operations, and posttransform back to the original orientation.
> Finally, grompp/mdrun should probably be made capable to rotate and
> lattice-reduce a box to have the internal representation during the MD
> run as optimized as possible).

OK, so then rotating the coordinates but not rotating the box 
invalidates the PBC. I think it would then make sense to remove the box 
from the output after rotation.

-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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