annealing
Some comments on the comments about annealing:
"Simulated Annealing is a Monte Carlo ("random draw",
"throwing the
dice") method
The basis of annealing is the heating up and cooling of something
to reach a globally lower energy. In the simulation context, Monte
Carlo is one method that might be used for annealing or other purposes.
The other method that I am familiar with is dynamics. In the general
sense then, the high temperatures can be simulated by either random
or deterministic methods.
In fact, as I understand it, 'annealing' has been generalized to
encompass any method in which normal conditions have been permuted
temporarily to enable an energy barrier to be crossed, i.e. futzing
with other things than temperature, and in contexts where temperature
does not exist. In the molecular context, lowering the torsional potentials
for a period and then turning them back on would be an annealing protocol.
"No SA option is provided (even) in the last version of Charmm,
Charmm - Version 22.0.b - April, 1991, I have recently used.
Neither is it available with the Amber or Ecepp force fields."
From what I have said above, it should be clear that annealing has
Some clips from the manual:
This is a guide to sander, a new AMBER module which allows
NMR-NOE refinement. The acronym stands for Simulated Annealing
with NMR-Derived Energy Restraints. The features described
below allow one to "easily" carry out refinements using NOE-
derived restraint distances, torsion angle restraints, and
penalty functions based on chemical shifts and NOESY volumes.
Sander also offer an excellent interface to protocols such as
simulated annealing, etc., ...
Also in the ../dat/nmr directory is a script,
mk_chir_cons, which creates constraints relating to chirality
and peptide bonds. Use of these constraints will ensure that
high-temperature annealing runs do not destroy chirality or
flip peptide bonds.
Bill Ross