From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Wed Jul 20 2011 - 12:25:18 CDT
Dear Jim,
Many thanks for providing with the hint, but eventually I was able
to execute the simulated annealing cycle I described in my previous email
via a C-shell script.
For anyone interested I might post my (not very elegant) script to
the mailing list.
Best regards,
M
2011/7/20 Jim Phillips <jim_at_ks.uiuc.edu>:
>
> It helps to provide the errors your script produces, but I'm going to assume
> these lines are your problem:
>
> outputName min_$i
> restartfreq $minCoorSteps
>
> You can't change outputName or restartFreq during a run (after the first
> "run" or "minimize" command triggers startup). If you just want to save the
> system state to files you should use the output command:
>
> output min_$i
>
> -Jim
>
>
> On Tue, 21 Jun 2011, Massimiliano Porrini wrote:
>
>> Dear all,
>>
>> I would like to implement the following simulated annealing
>> protocol:
>>
>>
>> WHILE i <= 1000
>> DO
>> - heating from 0K up to 800K
>> - dynamics at 800K
>> - cooling from 800 K to 0 K
>> - minimization and storing of the structure
>> END
>>
>>
>> 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,
>> MP
>>
>>
>> --
>> 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
>> mozz76_at_gmail.com
>> maxp_at_iesl.forth.gr
>
-- 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 mozz76_at_gmail.com maxp_at_iesl.forth.gr
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