rpath_generator
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.
[INPUT] 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 [OUTPUT] pdbfile = {}.pdb # pdb files used as reffile for string method rstfile = {}.rst # restart files used for string method [OPTION] nreplica = 4 # number of replicas