Re: simulated annealing with explicit water

From: Peter Freddolino (
Date: Mon Apr 24 2006 - 10:22:03 CDT

Hi Michel,
NAMD can be used to perform annealing dynamics; this is usually best
done using NAMD's temperature reassignment features
to heat and cool the system. Using these parameters, you can easily
specify a starting and ending temperature, and the increments at which
it changes.


L. Michel Espinoza-Fonseca wrote:

>Dear all,
>I've been looking for some information about running simulated
>annealing of a protein in explicit water with NAMD, but I didn't find
>any information. I would like to know if any of you have tried to
>perform such simulation.
>Thanks a lot!

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