pmf_analysis generate inputs for string method calculation from Targeted MD data. This utility is expected to be used after targetd MD simulation for generating an initial pathway for subsequent string method calculation.

cvfile       = cv.cv          # collective variable file
dcdfile      = run.dcd        # trajectory file of coordinates
dcdvelfile   = run.dvl        # trajectory file of velocities
prmtopfile   = 1ake.top       # amber parmtop file
pdbfile      = 1ake.pdb       # pdb file
pdbfile      = {}.pdb       # pdb files used as reffile for string method
rstfile      = {}.rst       # restart files used for string method
nreplica     = 4             # number of replicas