OpenMM does not give progress for minimization, just wait... RNA-test_mdr.pdb ... 1 nm Energy at Minima is -194414.222 kcal/mol saved RNA-test_mdr_min.pdb Cmd: rna_minimize.py -sp RNA-test_mdr.pdb Execution time: 257:07:11.893 start: 17:12:01 end: 10:19:13 DONE!