Originally prepared by Terra Sztain and Surl-Hee Ahn for spike WE simulations
with Amber simulation engine
Has been further revised for minimal adaptive binning (MAB) scheme
and WESTPA 2.0 by Surl-Hee Ahn
These scripts can be used and adapted for other WE simulations
- CONFIG: contains files needed to start the simulation for each segment/walker
- bstates: contains initial starting structures ("basis states") for the WE simulation
- BASIS_STATES lists bstates with probabilities/weights
- analysis.cpptraj is used during runseg.sh to extract progress coordinate and auxdata values at each iteration
- env.sh sets up the computing environment
- get_pcoord.sh extracts the progress coordinate values for the initial starting structures (only used for the very first iteration)
- init.sh is used to initialize the WE simulation (only used for the very first iteration)
- node.sh is used to run the simulations for each node
- post_iter.sh is used at the post-processing step of each iteration (usually to tar and compress seg_logs and traj_segs)
- runseg.sh is used to run each segment/walker at each iteration
- runwe.sh is the main script to submit on the supercomputer cluster to execute the WE simulation
- west.cfg is the main configuration file for the WE simulation that sets up the number of progress coordinates, number of iterations, etc.