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