Use average persistence length of parent segments in model.simulate(), rather than object returned _get_parent(), which can be 'model'; thanks to Elija Feigl

Revert "Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used"

This reverts commit 0fdd92dc.

Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used

Added option to specify custom persistence length to mrdna script for first 25% of coarse simulation

Expose enrg_md_steps option in mrdna and enrgmd scripts and in mrdna.simulate.multiresolution_simulation(); thanks to Elija Feigl for the suggestion

Added fill_sequence parameter to SegmentModel.set_sequence and to the mrdna and enrgmd scripts, with default value 'T', since that is most common for origami. Thanks to Elija Feigl for recommending the change.

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step

Added support for reading in orientation; added enrgmd script for output enrgmd files without running simulations