Energy Minimization Simulation

From: 김민재 (
Date: Fri Feb 22 2019 - 12:09:38 CST


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

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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