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Basic analysis for NAMD trajectories
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.
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Sample scripts for basic tasks in CHARMM
The scripts.tar.gz tar ball contains following scripts, along with a small set of auxiliary (data) files. These scripts are also available on this link, and questions about how to use these scripts are addressed in this thread on the CHARMM forums.
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VMD TCL script to calculate density profile normal to z-axis
denprofile_analysis.tcl TCL script for VMD to calculate density profile normal to z-axis. Run the script with argument "usage" for more info, or see following example:
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Basic and miscellaneous scripts
autocorr.awk AWK script to calculate autocorrelation of a time series.
histogram_dec.awk AWK script to create histogram.
histogram_discrete.awk AWK script to create histogram of discrete values (e.g. a variable taking integral values).
bootstrap_mean.awk AWK script to re-sample mean values in the bootstrap method.
runavg.awk AWK script to calculate running average of energy from NAMD output. Requires setting variables at command line.
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