This page is designed to serve as a repository for files that may be useful to group members. For information on uploading files, see notes below.
Queue submission scripts.
The apoa.sh model script is for a 8-processor job in NAMD, while the multiple_images.sh script is for 8 single-processor jobs in NAMD.
MD Analysis scripts
Basic analysis for NAMD trajectories
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Note that the -psf PSFfile topology description could be replaced with other filetype/filename options, e.g. -parm AMBERparmfile. Bin width and number are specified in the script, although they could be adjusted to be set at command line.
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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Notes on uploading files
When uploading scripts, please remember that comments are essential to helping others understand your work. All uploaded files should include author information, a date or version number, a description of the file's purpose and methodology, a description of the expected input (if applicable), and a description of the output format.
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