No longer recycle at unbound state
@@ -13,7 +13,7 @@ source env.sh
# Make sure that WESTPA is not already running. Running two instances of
# WESTPA on a single node/machine can cause problems.
-# This code will kill any WESTPA process that is currently running.
+# The following line will kill any WESTPA process that is currently running.
pkill -9 -f w_run
# Make sure that seg_logs (log files for each westpa segment), traj_segs (data
@@ -24,9 +24,12 @@ mkdir seg_logs traj_segs istates
# Define the arguments for the basis states (used for generating initial
# states; in this case we only have one), and target states (used for
-# knowing when to recycle trajectories).
+# knowing when to recycle trajectories). In this example, we recycle
+# trajectories as they reach the bound state; we focus on sampling
+# the binding process (and not the unbinding process).
+
BSTATE_ARGS="--bstate-file bstates/bstates.txt"
-TSTATE_ARGS="--tstate bound,1.8 --tstate unbound,16.9"
+TSTATE_ARGS="--tstate bound,1.8"
# Initialize the simulation, creating the main WESTPA data file (west.h5)
# The "$@" lets us take any arguments that were passed to init.sh at the
