simulated annealing

From: genie lfs (lfs.use_at_gmail.com)
Date: Mon May 01 2006 - 11:04:35 CDT

hello all..

generally in a simulated annealing we introduce constraints (eg
derived from NMR )
to constraint the search space and to arrive at the minimal energy
structure following the constraints..

can we do a unconstrained simulated annealing using md simulation with
namd.. i have seen threads on that and nothing about constrainsis
mentioned..

if i have to provide a constraint how can i do that?.. in my case i am
trying to simulate a small peptide folding with a disulphide bond as a
constraint....
can this be done ?

thank you
santhu

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