Added a new question to FAQ
@@ -4,7 +4,8 @@ Frequently asked questions (FAQ)
Simulation
-----------
-- How can I cleanly shutdown a simulation (without corrupting
+- How can I cleanly shutdown a simulation (without corrupting the h5
+ file)?
It is generally safe to shutdown a WESTPA simulation by simply canceling
the job through your queue management. However, to ensure data integrity
@@ -65,6 +66,22 @@ available on the web or the user manual for these packages make the
trajectories. As such, some of their guidelines for handling periodic
boundary conditions may not be applicable.
+- My WESTPA simulation crashed and nth iteration wasn't complete, how
+ can I continue from the nth iteration?
+
+In general restarting a westpa simulation will restart an incomplete
+iteration, retaining data from segments that have completed and
+re-running segments that were incomplete (or never started).
+
+In case that the iteration data got corrupted or you want to go
+back to an specific iteration and change something, you need to
+delete all the trajectory secgments and other files related to that
+iteration and run w_truncate on that iteration. This will delete westpa's
+information about the nth iteration, which includes which segments have
+run and which have not. Then restarting your westpa simulation will
+restart that iteration afresh.
+
+
GROMACS
--------
