Skip to content

Contribution ideas

Jump to bottom
Aaron Virshup edited this page Oct 3, 2016 · 6 revisions

Science

  1. RNA navigation - MDT has the capability to traverse many DNA and amino acid polymers, using methods such as residue.next(), chain.n_terminus, and chain.fiveprime_end. Additionally, the atoms in these polymers can be grouped via residue.backbone and residue.sidechain. We need the same capabilities for RNA!

  2. Electronic analysis - MDT is able to both calculate and visualize wavefunction amplitudes; it should do the same for total electron density. From that point, it would be great to do the same for other electron-density-based information like Fukui Functions and non-covalent-interaction surfaces.

Software engineering

  1. Run MDT on an academic cluster - right now, MDT will run jobs locally on your laptop, or on the cloud. How can users take advantage of academic HPC clusters? The solution will likely involve adding the following capabilities to Autodesk/py-cloud-compute-cannon:
  • singularity containers, and
  • an external library that allows us to work abstractly with different job schedulers (SGE, SLURM, Condor, etc.)

  1. Integration architecture - how can we make it as easy as possible to integrate new methods into MDT? For instance, if someone wanted to run and analyze LAMMPS dynamics from MDT, what's the most intuitive, least effort way of doing so? One possibility involves using CookieCutter github respositories as templates.

  2. Making sure the methods work - MDT has unit- and end-to-end-testing for much of its functionality, but we need tests to make sure external methods are integrated and working correctly. This means testing whether an RHF/STO-3G calculation returns the "right" result and whether our ForceField packages all return the same energy for a given forcefield and geometry.

Integrations

These are methods and pieces of software that should probably be pulled in from a mature package, rather than re-implementing them. This will likely involve:

  1. QM laundry list: semiempirical methods; support density fitting; allow users to create and configure hybrid density functionals; MCSCF with gradients; coupled cluster methods

  2. MM laundry list - CHARMM forcefields, OPLS forcefields, AMOEBA forcefields, QM/MM

Clone this wiki locally