[gmx-users] protein in a crystal

[Daan van Aalten]

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?

Daan

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...
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>