Updated run script to remove unneeded simulation steps and make fine-resolution model run longer; also added dependency on pynvml to query gpus

Made atomic simulation box smaller, because it's usually too big, causing namd to crash; TODO: calculate size from object

Conflicts:
	atomicModel.py

Updated interhelical bond exclusions to be consistent with ENRG MD server; no bonds within 10 angstroms of crossover

Fixed how atoms are indexed to allow interhelical bonds when insertions/deletions are staggered; generalized algorithms for finding indices between crossovers

Updated bead model handling of extra interhelical bonds due to crossovers between distant segments; now works for single crossovers

Updated orientation of ssDNA in atomic model so that z-axis is aligned with vector connecting adjacent nts; untested