Generic md class

[kristofarkas]

The problem is: that we want gromacs.Run and namd.Run (and potentially all other engine classes) to be convertible between each other, i.e. md_gromacs = gmx.Run(md=md_namd) or something like that should work.

The original idea was to make some kind of abstract superclass that contains all the attributes from gromacs and namd configuration files, but the two are too dissimilar for this approach to work. Some parts translate very nicely (1:1), but some don't. This is why there are separate modules for each.

The "solution" was to have some kind of generic md class which has all the attributes one can imagine, and then every actual md class cherry-picks the ones it understands (going through a converter).

To be honest, I'm not sure if this is the best way to do it. See what happens once I start implementing it.