Development version of plumed 2
scalable molecular simulation
How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation
How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.
Molecular Dynamics - Simulation Analysis and Preparation Suite
Auxiliary tools and scripts initially made for my PhD projects.
Torch artificial neural network function for plumed2
A small collection of function to postprocess plumed benchmark output
A small tutorial for using plumed benchmark
Short and simple introduction to developing parallel CVs in plumed2
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