“A command-line interface designed to perform complex workflows with few inputs”
By Alberto Cuzzolin
Nowadays, Molecular Dynamics (MD) simulation is known to be an important tool in drug discovery process. Although its potential is clearly proved, it is still not trivial to handle all the steps necessary to retrieve results. To handle all these aspects, we developed HTMD, a python framework that manages all these aspects and allows an easily scale up to an high-throughput manner.
Despite HTMD provides all the necessary functionalities, we decided to develop automated workflows, called “protocols or flows” that will ease and standardize the use of HTMD features. A command-line interface was designed to perform complex workflows with few inputs, allowing the user to customize its own protocol.
Several protocols are available with their specific options that the user can play with.
While the interface is simple and fixed (few options are available), Acellera Flows provide enhanced flexibility through template generation, meaning that the entire workflow is saved in pure python script.
At the moment, 4 protocols are available:
- Build Flow: A protocol to build systems with amber and charmm.
- SimpleRun Flow: A protocol to equilibrate and run MD simulation
- RunAdaptLig Flow: A protocol to run adaptive sampling for ligand-protein recognition
- CheckAdaptLig FLow: A protocol to analyze the ligand-protein adaptive simulation
- RunAdaptProt Flow: A protocol to run adaptive sampling for protein conformation
- MembraneBuilder Flow: A protocol to prepare phospholipid bilayer
- CheckAdaptProtFlow: A protocol to analyze the protein adaptive simulations
For more details, please visit our software website.