[gmx-users] Simulated Annealing

[Anton Feenstra]

>>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 releas 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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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