VoronoiAnalysis
madgal
Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.
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5 data points · 2022-06-01 → 2026-04-01How do you feel about this project?
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Question copied to clipboardWhat is the madgal/VoronoiAnalysis GitHub project? Description: "Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.". Written in Python. Explain what it does, its main use cases, key features, and who would benefit from using it.
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