[gmx-users] NMA

[Anton Feenstra]

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?
> and maybe it can work with shorter minimizations?

Why not run a short MD and do Essential Dynamics analysis?

Use g_covar for the covariance analysis, and g_anaeig for
display/projection of the results. IMHO, for a protein, this
gives more realistic results for the dynamics of the system
than a normal modes analysis.

If you're worried about getting out of a local minimum,
you could always run the MD at low temperatures, say 100K.
(Don't know if that has been done previously by someone.)

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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