Performs an Adaptive Sampling Run of a Ligand interacting with a Protein.
The Adaptive Sampling MD is a method that allows faster exploration of the conformational space available. In this flow, it is applied to the interaction of a ligand with a protein.
Get the data for running the RunAdaptLig flow examples here.
There, a generators folder for an Amber simulation can be found.
Run Adaptive Sampling for Ligand - Protein using contacts
To run an Adaptive Sampling MD batch consisting of 3 epochs for the ligand MOL and using contact as a metric, one can use the following command:
aceflow RunAdaptLig --inputdir runadaptlig/generators_amber --adaptligdir test_runadaptlig --numepochs 3 --numreps 2 --metric contacts --ligresname MOL --execmode Local