[gmx-users] protein in a crystal

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Mon Nov 29 11:09:13 CET 2004

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?


On Sun, 28 Nov 2004, Raul wrote:

> Hello, I want to set up a simulation of a protein in its crystal
> environment, so I have created a pbd of its unit cell to use as a
> starting point for dynamics. However some of the proteins have portions
> that are outside of the unit cell. So I have been wondering what is the
> right set of pbc conditions to use. Ive read the manual and the
> discussion list and I still cant make it out...
> When setting up the systme with editconf should I use -nopbc or -pbc,
> (please explain the difference)
> In the mdp file should I use pbc=xyz or pbc=full, (does this change the
> behavior of covalent interactions that cross the box?)
> Thanks I appreciate any assistance...
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