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Hi all,
<br>Thanks alot for your reply,
<br>I only want to see global motions of the bacbone or C-alpha , starting
from a
<br>2.7 A. resolution structure, so maybe it is impossible to minimize
until Fmax < 0.0001?
<br>and maybe it can work with shorter minimizations?
<br>Thanks again,
<br>with best regards,
<br>Ruben
<br>
<p>Bert de Groot wrote:
<blockquote TYPE=CITE>Ruben Martinez Buey wrote:
<br>>
<br>> Hi all,
<br>> 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?
<p>-this is a known problem in NM calculations. the minimization can take
<br>more time than the actual calculation and diagonalization of the Hessian
<br>-you don't HAVE to minimize until Fmax < 0.0001, but the risk is
larger
<br>that you end up with negative eigenvalues (one per saddlepoint instead
<br>of minimum). Again, this is not necessarily a problem, as long as you
<br>are aware of this and treat it in the appropriate way.
<p>Ways to make the minimisation faster:
<br>-start closer to a minimum, e.g. by doing a short relaxation MD or
<br> simulated annealing to zero K.
<br>-use a faster machine.
<p>--
<p>Bert
<p>____________________________________________________________________________
<br>Dr. Bert de Groot
<p>Max Planck Institute for Biophysical Chemistry
<br>Theoretical molecular biophysics group
<br>Am Fassberg 11
<br>37077 Goettingen, Germany
<p>tel: +49-551-2011306, fax: +49-551-2011089
<p>email: bgroot@gwdg.de
<br><a href="http://www.mpibpc.gwdg.de/abteilungen/071/bgroot">http://www.mpibpc.gwdg.de/abteilungen/071/bgroot</a>
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<pre>--
___________________________________________
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</pre>
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