OpenMM does not give progress for minimization, just wait... 4way-GCGA.pdb ... 1 nm Energy at Minima is -160747.504 kcal/mol saved 4way-GCGA_min.pdb Cmd: rna_minimize.py -sp 4way-GCGA.pdb Execution time: 199:23:59.630 start: 07:20:30 end: 14:44:29 DONE!