[gmx-users] Simulated annealing (SA) - protein or solvated protein?

[Nuno R. L. Ferreira]

Hello gmx's

A rather different question than the last one.
I read in a recent article from Dr. Tieleman's group, that they did a
restrained SA run on a built alpha-helix (to relieve bad contacts on atoms
of the side-chains), before the equilibration and production part of the MD
run.
My question is. What you guys think about doing the restrained SA in a
system with just the protein, or in a system with the protein solvated?
What is the best way, if there is one? In the former case, I think I would
have to use the gromos vacuum force field.

Regards,
NUno

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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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