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.

MD Analysis scripts

Sample scripts for basic tasks in CHARMM

The scripts.tar.gz tar ball contains following scripts:

There is also a small set of auxiliary (data) files.

http://www.biosci.ki.se/md/charmm.html These scripts are available on this link.
http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=186#Post186 If you have questions about how to use these scripts or any issues associated with them, please follow this thread on the CHARMM forum.

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:

vmd -dispdev text -psf system.psf -dcd sample_run.dcd -args seltext "not water" outfile zinfo_timeseries.txt histfile denprofile.txt first 100000 last 200000 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.

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.

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.

To upload: Choose "Attachment" under the "Add" menu at right.  Then, link to the attached file in this page using the following wiki syntax: \[\^filename.sh\], followed by a description of the file.

To use: download the file. Note that some browsers will append unwanted extensions to downloaded files. Remember that all every user is responsible for understanding at a detailed level all the tools that he/she uses!