[gmx-users] Simulated Annealing

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Wed Jan 21 09:55:02 CET 2004

Sounds interesting. Would you, please, elaborate or perhaps send me the 
part of the mdp file that programs the gradual release?

Thank you.


Anton Feenstra wrote:

>>> 4) How would I encode the gradual release of the [TM_C-alpha] group 
>>> at the last stage of the protocol?
>> Not implemented, you'd want the force constant of the restraint to go to
>> zero slowly, but there is no way currently. You can however just use a
>> lower force constant (by rerunning genpr).
> Also, you could consider releasing different groups of atoms in several
> steps, i.e. define a 'core' region, then first release the non-core side
> chains only, then the non-core backbone as well, then the core sidechains
> and finally all. I've done something similar in the final stages of
> optimizing a homology model.

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