Simulated Annealing with many frequent restarts

From: Phillips, Carolyn L. (
Date: Thu Apr 30 2015 - 18:51:19 CDT

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?


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