OpenMM does not give progress for minimization, just wait... rna_composer.pdb ... 1 nm Energy at Minima is -260640.012 kcal/mol saved rna_composer_min.pdb Cmd: rna_minimize.py -sp rna_composer.pdb Execution time: 287:15:48.840 start: 12:42:31 end: 12:58:20 DONE!