MD Anisotropy is a collection of Python tools for determining anistropic diffusion in Molecular Dynamics.
In its current form, there is no need to install the package. It consist of standalone scripts that can be executed in a workflow.
To determine the anisotropy of a simulated particle, the following steps must be made:
-
determine rotation matrix: the rotation matrix is the operation that must be performed on the current configuration to align it with a reference (in the least squares sense). This can be performed by
gmx rotmat. -
calculate fixed (but arbitrary) angle MSD (FA-MSD): the fixed-angle MSD calculates the full MSD Tensor relative to a fixed initial angle, at lagtime = 0. There are two marginal cases of interest:
- When the major axis of the diffusing particle in the reference configuration aligns with the laboratory X axis, then at small lagtimes the MSD along X and Y will be uncorrelated, with larger MSD along the X axis.
- When the major axis is at 45 degrees, the initial displacements along X and Y will be completely correlated.
python diffusion_tensor.py reference.gro traj.xtc rotmat.xvg MSDtensor.dat- calculate the principal axes of anisotropiy diffusion: The task of determining the principal axes of diffusion is then performed by calculating the eigenvectors and eigenvalues of the FA-MSD at a given lagtime. At small lagtimes, the difference between the axes is representative of the anisotropy, which should vanish in the long lag-time limit. However, because of the eigenvector determination, statistical errors are detected by the method and visible in the resulting curves as an apparent difference between the major and minor axes of diffusion.
python orient.py MSDtensor.dat MSDtensor-DIAG.dat