Opening NetCDF trajectory file '/u/ac/kw8cr/yank/test-systems/T4-lysozyme-L99A/amber-gbsa/amber-gbsa/1-methylpyrrole/results/new/complex.nc' for reading...
dimensions:
       iteration    10000
         replica        1
            atom     2616
         spatial        3
            seed        4
Read 10000 iterations, 1 states
Average state-to-state acceptance probabilities
(Probabilities less than 0.050000 shown as blank.)

          0 
   0  1.000 
Writing replica trajectories...

Working on state 0 / 1