Automate the dimensions of the System box

[shanilpanara]

Summary

At the moment, when we generate an oxDNA system, we are manually inputting an x, y and z size dimension for the box of the system (e.g. [50. , 50. , 50.]). For MD Simulations, we do not want those DNA strands to be outside of the so-called box of the system.

• Ideally, we would like the size of the box which is x2 the size of the largest length in the DNA Origami structure (I think... @debeshmandal definitely edit this if I'm recalling that wrong)

• The size of the box must be re-updated upon adding new strands to the system.

• We must also make sure, we can control the size of the box manually if we want and have the ability to disable this 'update the size of the box' feature too!

[debeshmandal]

This is a tricky one because I think that the box should in general be manually inputted since when running simulations, since it is so important to molecular simulations and a user would manually input the box size more often than not. I think we can add an option to the System class where it takes a variety of different arguments, e.g.:

• np.ndarray|list|tuple -> np.array([50., 50., 50.]) - manually describing x, y, z
• float|int -> 50. - a cubic box of 50.
• str -> 'auto' - automatically determine box size

[shanilpanara]

Another thing I've noticed is that the DNA structures are not 'centred' within this box, this might also be something we need to consider implementing alongside this.