[gmx-users] protein in a crystal

[Daan van Aalten]

Hi Anton

This is true, but consider the alternative - simulating the unit cell
rather than the asymmetric unit could allow significant conformational
differences between molecules that (on average!) have *exactly* the same
conformation in the crystal.
I also wouldn;t know what the best approach would be to the asymmetric
unit/unit cell size as pressure coupling could easily screw up the
crystal packing.

Daan


On Mon, 29 Nov 2004, Anton Feenstra wrote:

> Daan van Aalten wrote:
>
> > Hi Raul
> >
> > The only right way to do this is to use proper space group symmetry and
> > not expand to the full unit cell (assuming you are not already in P1 :-)),
> > so simulate the crystallographic asymmetric unit.
> > I think Bert de Groot has implemented a subset of space groups in GMX -
> > perhaps he can give you some hints?
>
> but be aware that simulating only one asymmetric unit can (will!) severely
> underestimate fluctuations since all units are forced (by definition) to be
> completely identical while in the real crystal they (obviously!) are not.
>
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
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