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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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USAGE: vmd -psf PSFfilesystem.psf -dcd DCDfilesample_run.dcd -args seltext "not water" outfile OUTPUTFILENAMEzinfo_timeseries.txt histfile HISTFILENAMEdenprofile.txt [ first FIRST_FRAME ] [ 100000 last LAST_FRAME ] [200000 freq FRAME_FREQ ]100 |
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.
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