[gmx-users] NMA

[Ruben Martinez Buey]

Hi all,
Thanks alot for your reply,
I only want to see global motions of the bacbone or C-alpha , starting from a
2.7 A. resolution structure, so maybe it is impossible to minimize until  Fmax < 0.0001?
and maybe it can work with shorter minimizations?
Thanks again,
with best regards,
Ruben


Bert de Groot wrote:

> Ruben Martinez Buey wrote:
> >
> > Hi all,
> > I am trying to energy minimize my protein+ligand (5000 atoms) for a further NMA. Anyway, if the c, 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
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--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144,  28006  MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18


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