Simulation container object

[tomnewport]

Most processes one might want to do involve:

• Modify a structure, topology and parameters.
• grompp a structure (gro), topology (top), parameters (map) to get a preprocessed binary file tpr
• mdrun the tpr to get a trajectory and a structure

The simulation container will be based around the grompp step. Several GROMACS commands produce files in the working directory.

structure = GROFile("structure.gro")
topology = TOPFile("topol.top")
em_mdp = MDPFile("em.mdp")
md_mdp = mdp.MD_MDP

s = SimulationContainer()
s.add(structure)
s.add(topology)
s.add(em_mdp)

em = s.folder("em")
em.gromacs.grompp(c="/structure.gro", p="/topol.top", f="/em.mdp", o="em.tpr")
em.gromacs.mdrun(deffnm="em")

md = s.folder("md")
s.md.gromacs.grompp(c="/em/em.gro", f="/md.mdp" p="/topol.top")
s.md.bash("echo llama >> llama.txt")
s.md.bash(["echo", "llama"])

In the future this container could also keep a json dictionary to store:

• All commands performed in the container (in order, including output, host, user, pid and exit code)
• All files which have been added to the container from elsewhere

It should also be possible to save and load a container. Later work could allow the container to resume after a crash, or synchronise with a server using SAGA.

Tasks:

• [x] Simple container with a GROMACS instance
• [x] Add file objects to the container
• [x] Create container folder object
• [x] Resolve file paths within container
• [x] Run GROMACS and bash within container (or folder)