simulated annealing protocol

From: Massimiliano Porrini (
Date: Tue Jun 21 2011 - 07:41:00 CDT

Dear all,

I would like to implement the following simulated annealing

WHILE i <= 1000
  - heating from 0K up to 800K
  - dynamics at 800K
  - cooling from 800 K to 0 K
  - minimization and storing of the structure

So that at the end of the simulation I get 1000 minimized structures.
Obviously I would like the final (minimized) structure of every cycle
to be the initial one
of the next cycle.

Is this possible with namd?

I tried to write a configuration file to achieve that, but in vain.
The file is enclosed in this email and the steps number of heating, dynamics,
cooling and minimizing are purely for testing.

Any help would be really appreciated.

Best wishes,

Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails :

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