A Python package to perform preliminary analysis of molecular dynamics trajectories. The source code can be found at: https://github.com/djmaity/md_davis
Create dynamic visualization of electric field around the molecule using PyMOL.
Create interactive plot for time series data: root mean squared deviation (RMSD) and radius of gyration
- Create Free energy landscapes using common ranges and number of bins.
- Create interactive plot of containing the following residue level properties:
- root mean squared fluctuation (RMSF)
- circular standard deviation of backbone dihedral angles
- Secondary structure
- Solvent accessible surface area
- Mean and standard deviation for the total surface electrostatic potential per residue
- Mean and standard deviation for the mean surface electrostatic potential per residue
It can also use an alignment to align the residue level data from different proteins along the x-axis. This ensures that the peaks line up properly for better interpretation.
Some instructions for creating these types of plots are available here: Instructions and instructions for calculating surface electrostatic potentials can be found here: Electrostatics
help for each command in MD Davis can be accessed with
-h, for example