OpenMM does not give progress for minimization, just wait... tetraloop_mdr.pdb ... 1 nm Energy at Minima is -14996.692 kcal/mol saved tetraloop_mdr_min.pdb Cmd: rna_minimize.py -sp tetraloop_mdr.pdb Execution time: 2:36:22.479 start: 21:20:37 end: 23:57:00 DONE!