From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Jul 20 2011 - 11:31:19 CDT
It helps to provide the errors your script produces, but I'm going to
assume these lines are your problem:
You can't change outputName or restartFreq during a run (after the first
"run" or "minimize" command triggers startup). If you just want to save
the system state to files you should use the output command:
On Tue, 21 Jun 2011, Massimiliano Porrini wrote:
> 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 : M.Porrini_at_ed.ac.uk
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