OpenMM does not give progress for minimization, just wait... c3c2c3_rosetta_mdr.pdb ... 1 nm Energy at Minima is -22737.862 kcal/mol saved c3c2c3_rosetta_mdr_min.pdb Cmd: rna_minimize.py -sp c3c2c3_rosetta_mdr.pdb Execution time: 0:12:49.551 start: 17:03:38 end: 17:16:28 DONE!