[gmx-users] protein in a crystal

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 29 09:10:36 CET 2004

On Sun, 2004-11-28 at 19:33 -0600, 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...

be sure to set the unit cell dimensions right. a proper pdbfile should
have a correct CRYST1 record.
> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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