Targeted Molecular Dynamics

From: Thomas Albers (
Date: Sat Jun 30 2012 - 14:56:53 CDT


I am not sure how to understand this sentence from the section on
Targeted Dynamics: "At each timestep, the RMS distance between the
current coordinates and the target structure is computed (after first
aligning the target structure to the current coordinates)."

Does this mean that NAMD aligns the target coordinates to the model at
the beginning of the dynamics run, or do I perform the alignment
before starting NAMD, and the program just calculates forces and


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