[gmx-users] CRY-ED question

Bert de Groot bgroot at gwdg.de
Tue Jul 27 18:43:31 CEST 2004

Daan van Aalten wrote:
> Hi Ruben
> No you can't. However what we have done in the past is to
> 1) fit your two crystal structures on your reference frame (of course
>    making sure they have the same atoms etc)
> 2) calculate a vector describing the structural transition in hyperspace
>    simply by subtracting the coordinates between the two structures
> 3) normalize (!!!) this vector

in fact, you could use g_covar to do these three steps, provided you start
from a nmr-style pdb file (or xtc or any other trajectory format gromacs
supports) containing your two x-ray structures. This would have the advantage that
it's directly compatible to MD output and can be directly analysed by e.g.

It's important, as Daan said, to make sure that you have the same atoms and
same ordering for both structures. You'll notice when you use g_anaeig afterwards if
something went wrong though.

> 4) now you can project your ED eigenvectors onto this vector to see if
>    the experimentally observed conformation change is at all covered by
>    your MD simulation!
> Daan


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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