From: Andrew Doig (
Date: Thu Feb 02 2023 - 19:07:57 CST


I have been working my way through the 2015 "Modeling Nanopores for
Sequencing DNA" tutorial as a first step to understanding MD work.

I have encountered an error.

In the section 3.2.13 "Minimize the system" I have run namd with the
min.namd config file as described in the tutorial. The next step is to run
another minimization but with the config file min2.namd.

Unfortunately this "min2.namd" config file appears to be missing.
"min.namd" is provided with the protocols but min2.namd file does not
appear to be.

Does anyone have insight into how to locate or generate this file?

Thank you,