A simple set of functions to extract physical frames from and visualize Multi-Site Lambda Dynamics (MSLD) trajectories generated from Adaptive Landscape Flattening (ALF)1.
These functions take in many system specific variables generated by MSLD-py-prep2, as well as lambda trajectory files (typically a .dat file in the ALF production analysis directory), and a .dcd MSLD trajectory file generated by CHARMM.
The output is either a PyMOL visualization of the lambda trajectory (using the transparency setting) via the visualize_pymol function, or, a directory called run{i}_frames containing subdirectories of each physical ligand's frames throughout the trajectory via the grab_frames function. Both of these functions use the output of get_subs_on.
These scripts can be run from within the ALF directory where the trajectory to be visualized was created.
1J. Phys. Chem. B. 2017, 121, 15, 3626–3635
2J. Chem. Inf. Model. 2022, 62, 6, 1479–1488
- Python 3 or later versions
- PyMOL
- pyCHARMM
Luis F. Cervantes and Furyal Ahmed