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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. 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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