[gmx-users] protein in a crystal

[David van der Spoel]

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...
pbc=xyz

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...
> 
> _______________________________________________
> 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.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++