add function to write trajectory with fixed box size

[orbeckst]

Is your feature request related to a problem?

Writing the universe with all conformers with

u.atoms.write("output.trr", frames="all")

creates a trajectory without a box. This may be a problem for re-evaluating energies in GROMACS with cutoffs as this needs periodic boundary conditions.

The box can be added afterwards with a MDAnalysis on the fly transformation (set box dimensions

box = np.array([15, 15, 15, 90, 90, 90])
u.add_transformation(mda.transformations.boxdimensions.set_dimensions(box))
u.atoms.write("boxed.trr")

(or setting the box dimensions in a loop while writing a new trajectory) but

1. We don't always know the right box dimensions (maybe the molecules is too big?)
2. It's tedious...

Describe the solution you'd like

Add a function molconfgen.output.write_pbc_trajectory(u, filename, box=None) that

1. takes a universe with conformers u
2. filename: trajectory filename
3. optional box argument
   • None: no box (no PBC)
   • "auto": find a "good" box (define what that means ...)
   • float: cubic box with length box (and fail if box size is not safe)
   • [A, B, C, alpha, beta, gamma]: regular box description (and fail if not safe)

Describe alternatives you've considered

Do it manually ...