RE: Energy Minimization Simulation

From: Vermaas, Joshua (
Date: Fri Feb 22 2019 - 12:55:37 CST

Before minimizers were as good as they are, bleeding off extra energy coming from badly minimized structures at low temperature was pretty common. In NAMD, 99% of the time I can get away with one combined minimization/equilibration run:

minimize 1000
reinitvels $temperaturegoeshere
run $howevermanystepsyouwant

After that, you'd use the restarts to begin your data collection in a real production run.


On 2019-02-22 11:14:46-07:00 wrote:

I am currently trying to run a MD simulation for a period boundary system of a solvated protein. I have read through the namd tutorial and user guide. However, I was wondering about how exactly I would have to proceed with the molecular dynamics.
The above link tells me to run 4 independent runs. I was actually planning on running only two: an energy minimization and an equilibriation. Can anyone explain why one would have to run separate 'heating' and 'production' simulations (I thought that an equilibriation, or at least the simulation the namd tutorial template produced, covered both of these processes.)
Also, I would really appreciate it if someone could check and see if the configuration templates for energy minimization provided on the above site were reliable.

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