Re: Simulated Annealing with many frequent restarts

From: Maxim Belkin (
Date: Fri May 01 2015 - 09:46:21 CDT


NAMD behavior depends on how you actually "ramp up" the temperature and
what you mean by "restart automatically". If you use
"reassignTemp/reassignFreq/reassignIncr/reassignHold" in conjunction
with "firsttimestep" then NAMD should restart with correct temperature.
If you use your own tcl script along with "rescaleTemp", then you have
to take care of everything yourself.

"restartsave" does not do anything special in this regard as it only
allows you to restart a simulation from an arbitrary point in the past
and requires a little bit of tcl scripting.


P.S. "firsttimestep" should be set to the last step in the
halted/aborted simulation at which NAMD wrote restart files.

On 04/30/2015 06:51 PM, Phillips, Carolyn L. wrote:
> I apologize if this has been answered before but searching the user list + manual has not answered this for me.
> I want to do a simulated annealing of a system. It would seems this can be done by temperature reassignment. However, I also am working with a wallclock limit that means I need to restart my simulation with fairly high frequency. What I cannot figure out is whether NAMD can correctly return to the specified temperature schedule when restarted automatically. For example, if the temperature is ramping from 300K to 350K by incrementing by 10K every 1000 time steps, and the simulation is restarted after 20001 time steps, will the temperature of the system revert to 300K or be at 320K? If I use “restartsave yes” does that do anything?
> Cheers,
> Carolyn

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