From: Ribi Akbar (
Date: Mon May 23 2022 - 18:54:41 CDT


I am wondering how namd can extract the structure of protein after
equilibration step. It becomes very important, for instance, when we want
to perform molecular docking that requires the stable structure of the
protein. Therefore, we might want to run an equilibration step to obtain
such a stable structure. In Amber, there is a clustering method that can
evaluate the most stable structure over time in the trajectories. But, I
have no idea how to do so in namd. Thanks

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