[gmx-users] Simulated annealing 10000K

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Wed Jul 30 21:36:02 CEST 2003

There is a lot of literature about calculation of cyclic peptides by 
the group of Kessler in Munich. They do similar things to what Xavier 
describes, and use the clusters as input for free MD in water. But they 
normally do have NMR restraints...

On Wednesday, July 30, 2003, at 10:30 PM, Xavier Periole wrote:

> Yop, sorry I meant 1000 K. 10000 K is way too much.
> Marco is right. With 11 residues it is unlikely that your peptide has 
> a unique
> conformation in solvent. It probably explore different conformations 
> with diffenrent
> probabilities.
> How did you generate your 10 structures with Modeler. I thought it 
> needed a
> template !! And what isthe point of doing an SA on a specific 
> conformation ?
> You loose it at 1000K anyway !!
> I did some thing similar where I generated 100 conf from SA with an 
> implicit
> solvent (faster) and after that I made clusters of them.
> XAvier
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
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