Update analyze command help message
@@ -43,9 +43,18 @@ Free Energy Required Arguments:
Free Energy Optional Arguments:
--skipunbiasing Skip the radially-symmetric restraint unbiasing. This can be an expensive step.
+ If this flag is not specified, and no cutoff is given, a distance cutoff is
+ automatically determined as the 99.9-percentile of the restraint distance distribution
+ in the bound state.
--distcutoff=DISTANCE The restraint distance cutoff (in angstroms) to be used to unbias the restraint.
+ When the restraint is unbiased, the analyzer discards all the samples for which the
+ distance between the restrained atoms is above this cutoff. Effectively, this is
+ equivalent to placing a hard wall potential at a restraint distance "distcutoff".
--energycutoff=ENERGY The restraint unitless potential energy cutoff (i.e. in kT) to be used to unbias the
- restraint.
+ restraint. When the restraint is unbiased, the analyzer discards all the samples for
+ which the restrain potential energy (in kT) is above this cutoff. Effectively, this is
+ equivalent to placing a hard wall potential at a restraint distance such that the
+ restraint potential energy is equal to "energycutoff".
YANK Health Report Arguments:
-o=REPORT, --output=REPORT Name of the health report Jupyter notebook or static file, can use a path + name as well
