We are working on some new workflows that will be added to the current list of workflows and launchers:
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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.
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Workflows for Free Energy Calculation (PMX):
- pmx_cv_cufix_term: Performs a fast-growth mutation free energy calculation from two equilibrium trajectories.
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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_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.
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.
