[gmx-users] Simulated annealing

[Marc Ceruso]

> my peptide have 11 aminoacids and it is cyclic.

So unless you have NMR data, what you're trying to do is predict the
structure of your peptdide from scratch?
In the latter case at best you will find ensembles of distinct conformers,
Maybe the papers van Gunsteren's group on the molecular dynamics of a
small peptide will help you :

Proteins. 2001 Apr 1;43(1):45-56.
Entropy calculations on a reversibly folding peptide: changes in solute
free energy cannot explain folding behavior.
Schafer H, Daura X, Mark AE, van Gunsteren WF


Marc