PyBILT
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LoLab-MSM
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
The file formats supported by PyBILT (i.e., the MDAnalysis backend) need to be documented, either in the README or ReadTheDocs pages. At the least, it should link back to the...
Currently PyBILT uses MDAnalysis as the backend for trajectory processing. It might be a nice upgrade to detach PyBILT from specifically needing MDAnalysis and allow it to use other trajectory...
Add computation of the dimensionless overlap parameter and interdigitation length from Chinmay Das, Massimo G. Noro, Peter D. Olmsted, Simulation Studies of Stratum Corneum Lipid Mixtures, Biophysical Journal, Volume 97,...
It would be nice to add protocols for the bilayer_analyzer to compute the bending modulus, as well as other moduli like the tilt and twist moduli. A protocol could be...
The modules in pybilt.lipid_grid currently don't have support for dealing with membrane embedded proteins, which means properties like area per lipid can't be accurately estimated for membrane embedded protein systems....
The BilayerAnalyzer class assumes that the coordinates of the input trajectory are wrapped by atom and therefore automatically unwraps the coordinates by atom. This can fail when the first frame...