BioExcel Building Blocks (BioBB) High Performance Computing (HPC) Workflow repository

We are working on some new workflows that will be added to the current list of workflows and launchers:

• Workflows for MD:

  • md_list: Performs a system setup and runs a molecular dynamics simulation on each one of the structures listed in the YAML properties file.
  • md_muts_sets: Performs a system setup and runs a molecular dynamics simulation for each one of the listed mutations in a given structure.
  • md_add_muts_wt: Applies a list of mutations over the initial structure obtaining a set of structures (initial structure + one mutation, initial structure + two mutations, initial structure + three mutations, ...). Finally performs a system setup and runs a molecular dynamics simulation for each of the structures in the set.

• Workflows for Free Energy Calculation (PMX):

  • pmx_cv_cufix_term: Performs a fast-growth mutation free energy calculation from two equilibrium trajectories.

• Launchers:

  • md_launch: Launcher for the md_list workflow.
  • mdmut_launch: Launcher for the md_muts_sets and md_add_muts_wt workflows.
  • pmx_launch: Launcher for the pmx_cv_cufix_term.

The launchers are available in: * Mare Nostrum IV (MN4) at the Barcelona Supercomputing Center (BSC)

Biobb modules used

• biobb_pmx: Tools to setup and run Alchemical Free Energy calculations.
• biobb_md: Tools to setup and run Molecular Dynamics simulations.
• biobb_analysis: Tools to analyse Molecular Dynamics trajectories.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

• (c) 2015-2020 Barcelona Supercomputing Center
• (c) 2015-2020 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.