[gmx-users] protein in a crystal
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Tue Nov 30 10:32:57 CET 2004
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
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.
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> | _ _ ___,| K. Anton Feenstra |
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