[gmx-users] Simulated annealing 10000K

Xavier Periole periole at inka.mssm.edu
Wed Jul 30 21:30:04 CEST 2003

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

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. 


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