[gmx-users] protein in a crystal

Raul raul at lima.wustl.edu
Mon Nov 29 02:33:41 CET 2004

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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