Getting Started - westpa/westpa GitHub Wiki
- Read the introduction to the weighted ensemble strategy and introduction to WESTPA.
- Work through the WESTPA tutorials in LiveCoMS (see related files here). Each time you set up a WESTPA simulation, complete the checklist.
- Defining and Calculating Progress Coordinates
- Data management, network, and disk usage
- Installing WESTPA
- Which work manager should I use?
- Running WESTPA on multiple nodes using ZMQ
- Quickly deploy WESTPA to check cluster settings.
- We recommend starting with an existing WESTPA simulation directory (e.g. from a tutorial or one from an experienced user) that most closely matches your use case rather than building a directory from scratch.
- Copy your basis state(s) into the
bstatesfolder and make sure that the name matches that in the bstates.txt file. If you want to use more than one basis state for your simulation, please see this page (coming soon...) for more detailed instructions on how to do that. - Copy your system topology and dynamics input file(s) into the
common_filesfolder. - Edit
env.shto make sure that all required programs are sourced and all required conda environments are activated. - Edit
west.cfgaccordingly to specify WE parameters. - If you want to run steady-state WE, make sure your
init.shhas the target state options defined and that you define that target state, either ininit.shor intstate.file. - Edit
run.slurmto conform with your specific hardware requirements. - Go into
westpa_scriptsand editget_pcoord.shandrunseg.shto have the correct names for your topology and bstate files, run dynamics using your specified resource and calculate a progress coordinate. - If your files are all ready to go, it's also possible to set up the WE simulation entirely with Python, as demonstrated by this Jupyter Notebook.