Allow zero eigenvector modes in the NMD file

Modify the writeNMD method in nmdfile.py with an
optional argument zeros, allowing zero eigenvector
modes to be written to the NMD file. It is sometimes
very useful to visually inspect the rigid-body motion
vectors of proteins, for instance in the context
of protein docking.

If zeros is **False** (by default), this function
skips modes with zero eigenvalues.

If zeros is **True**, modes with zero eigenvalues are
written out, their scaling factor being the square-root
of the inverse of the mode number times 0.0001. This
provides descending factors consistent with the NMA modes.
Merge branch 'writeNMDzeros' of https://github.com/toliwa/ProDy into writeNMDzeros

Conflicts:
	prody/dynamics/nmdfile.py