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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 density calculations are correct only for
Run with options "--usage" or "--help" for more details:
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Usage: basic_analysis.sh --name SIMNAME [ --logfile FILE ] [ --psf PSFFILE ] [ --outputdir ODR ] [ --dcdfreq N ] [ --rmsdsel SELTEXT ] Performs simple analysis tasks for simulation without output SIMNAME. OPTIONS: --logfile FILE : Use FILE as NAMD log file. Default value is SIMNAME.log --psf PSFFILE : Use PSFFILE (either CHARMM or AMBER format) as system topology file. Should have .psf or .parm7 extension for filetype recognition by VMD. Default value: SIMNAME.psf --outputdir ODR: Write analysis output to directory ODR. Figures will go to ODR/figures/. Default value: $(dirname SIMNAME)/analysis_output/ --dcdfreq N : Frequency at which frames were written to DCD file SIMNAME.dcd. Default 100. --rmsdsel SELTXT: VMD selection text for RMSD calculation. Must be enclosed in quotes. Default value: "all". |
Sample scripts for basic tasks in CHARMM
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