[gmx-users] NMA

[Bert de Groot]

Ruben Martinez Buey wrote:
> 
> Hi all,
> I am trying to energy minimize my protein+ligand (5000 atoms) for a further NMA. Anyway, if the Fmax must be < 0.0001, it´s very slow and it never ends on my single processor Silicon workstation... Is there any way to make it faster?


-this is a known problem in NM calculations. the minimization can take
more time than the actual calculation and diagonalization of the Hessian
-you don't HAVE to minimize until Fmax < 0.0001, but the risk is larger
that you end up with negative eigenvalues (one per saddlepoint instead
of minimum). Again, this is not necessarily a problem, as long as you
are aware of this and treat it in the appropriate way.

Ways to make the minimisation faster:
-start closer to a minimum, e.g. by doing a short relaxation MD or 
 simulated annealing to zero K.
-use a faster machine.

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________