atomate2 / OpenMM Enhancements: Added OPLS Support

[shehan807]

In the coming week, I plan to implement enhancements to the atomate2 / OpenMM features specifically through support for OPLS-based high-throughput pipelines. Any feedback or concern for overlap with existing efforts would be greatly appreciated:

1. Extend download_opls_xml to using BOSS v5.1 via Docker

Details mentioned here, to use BOSS v5.1 one requires a local install of the executable provided by the Jorgensen group. Given the number of dependencies to run the program (i.e., 32-bit compatible libraries), Docker images are suitable. I would defer to anyone who is more familiar with the licensing aspect of distributing code (here is the BOSS license: NonProfitLicense.pdf), but having a self-contained environment of ligpargen would seem easier than requiring users setting it up locally.

2. Implement Lennard-Jones OPLS combination rules via a Nonbonded flag

The CustomNonbondedForce in OpenMM implements the Lorentz-Berthelot combination rules to estimate sigma and epsilon parameters for 1-2, 1-3, and 1-4 interactions. However, correctly implementing the OPLS-AA geometric combination rules requires modification of the OpenMM system.

3. Add maker for conditional equilibration runs based on physical parameter

[dspoel]

I am just googling for OPLS combination rules in OpenMM. Wasn't that already implemented in OpenMM?
openmm/openmm#1918

[shehan807]

The NonbondedForce class still does not support alternate combining rules (openmm/openmm#4384 (comment)) nor does LigParGen create the necessary CustomNonbondedForce class when it generates .xml files. Instead, this is done via opls_lj(), as recommended by the LigParGen website and now implemented in PR #1111.