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
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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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
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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.
Sample scripts for basic tasks in CHARMM
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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 alculate 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:
| Code Block |
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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
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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
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