Hi,
On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote:
2. Is minimisation in GROMACS only used as a precursor to the md-
simulation to remove bad contacts, or can we also use it
effectively to minimize a raw modelled ab-initio structure.?
Well, technically you can of course use it, but any energy
minimization algorithm will only take you to a close local minimum in
the energy (=enthalpy) landscape.
If you want your model to get closer to the native state you need
refinement, and that's way more complicated. Search the literature
for techniques like simulated annealing, Replica-exchange molecular
dynamics, etc.
Cheers,
Erik
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php