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basic_analysis.sh A simple script for analyzing NAMD output files and trajectories. This script extracts energy, temperature, and pressure values from a simulation log file and plots them as a timeseries, along with running average of energy, RMSD of system and of a selection (specified at command line), and density. Users should feel free to adapt this script to their own needs.
Note that this requires runavg.awk, and density calculations are correct only for simulation cell types where Volume = a*b*c. Run with options "--usage" or "--help" for more details:
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