This is an example using a rate matrix corresponding to the master equation
from Jeremy Schmit's group.

Run GMIN first to fit the rates to corresponding free energy barriers and
stationary distribution. The data file needs the number of states, kT, and
(h/kT in s) /(unit of time in s) which is 1.5997D-13 s for SI units.
If the kT parameter is set to 1.0 then the free energies are dimensionless and in units of kT.
Then you set TEMPERATURE to 1.0D0 in pathdata. 
For energy in kcal/mol use kT=0.596 in data and TEMPERATURE 0.596 in pathdata.

The GMIN run should give min.data and ts.data files.

We can either use PATHSAMPLE with the FREEENERGY keyword  and set PLANCK to (h/kT in s) /(unit of time in s) = 1.5997D-13 s
or omit FREEENERGY, and leave PLANCK at default value of 1,
and use vibrational columns in ts.data and min.data, which GMIN writes as
0 for ts and 2*Log[2*Pi*kToverh*time] = 62.60 for the minima. 
For free energies in min.data and ts.data these formulations should agree!

