[gmx-users] NMA

Bert de Groot bgroot at gwdg.de
Wed Apr 9 08:55:01 CEST 2003

Ruben Martinez Buey wrote:
> 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?

no it should still be possible, but the nearest minimum may
be far away (especially if you run in vacuo). You can check how
the structure changes during the EM. In the ideal case the structure
shouldn't drift too much. If it does, then that's probably a sign
of a poor starting structure, or a forcefield/vacuum artefact.

> and maybe it can work with shorter minimizations?

perhaps. as I wrote before, it may be worth a try.
IIRC, I got fastest convergence for the EM when I started with steep and
then switched to cg, or even when doing iterative cycles of steep and cg.


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

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