viewSq is a utility for calculating, analyzing, and visualizing static structure factors (S(q)) from trajectories produced using molecular dynamics or Monte Carlo simulations.
A tutorial is available here.
If you find this code useful in your research, please cite:
- Add the following line to /usr/local/lib/vmd/scripts/vmd/loadplugins.tcl
vmd_install_extension viewsq viewsq_tk_cb "Analysis/viewSq"
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Copy the folder "viewsq1.0" to /usr/local/lib/vmd/plugins/noarch/tcl
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Copy the file "Calculate_rdf_stats_py.py" to /usr/local/lib/vmd/scripts/python
Invoke VMD and look for the plug-in under Extensions->Analysis.
Ensure Python 3.* is the default. If VMD asks for a path to Python, the following may work: /usr/bin/python3.
- Add the following line to /Applications/VMD 1.9.3.app/Contents/vmd/scripts/vmd/loadplugins.tcl
vmd_install_extension viewsq viewsq_tk_cb "Analysis/viewSq"
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Copy the folder "viewsq1.0" to /Applications/VMD 1.9.3.app/Contents/vmd/plugins/noarch/tcl
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Copy the file "Calculate_rdf_stats_py.py" to /Applications/VMD 1.9.3.app/Contents/vmd/scripts/python
Ensure Python 3.* is the default.
VMD 1.9.3 may not be compatible with recent MacOS versions: https://www.ks.uiuc.edu/Research/vmd/macosxcatalina.html
- Add the following line to \VMD\scripts\vmd\loadplugins.tcl
vmd_install_extension viewsq viewsq_tk_cb "Analysis/viewSq"
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Copy the folder "viewsq1.0" to \VMD\plugins\noarch\tcl
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Copy the file "Calculate_rdf_stats_py.py" to \VMD\scripts\python (the folder may need to be created manually)
Invoke VMD and look for the plug-in under Extensions->Analysis. When running viewSq, VMD may require you to specify the location of the Python script from step #3. Ensure Python 3.* is in the Windows path.
Note: 64-bit Linux versions of VMD with viewSq can also be run using Windows Subsystem for Linux (https://docs.microsoft.com/en-us/windows/wsl/install-win10) and an X server.
Invoke VMD and look for the viewSq module under Extensions->Analysis.
A tutorial is available here.
Copyright 2020 Travis Mackoy
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