Evan Pretti

Tutorial or cookbook entry describing the use of tabulated functions

5

I had been working on a Jupyter notebook describing how to use piecewise spline / tabulated function potentials in OpenMM. The original idea was for a cookbook entry just demonstrating...

Add constant potential method

3

See #4863 for discussion of features. Progress tracking for this draft PR: - [X] Public API - [x] Reference platform implementation - [x] CPU platform implementation - [ ] GPU-accelerated...

Inconsistent checking of exception parameter updates across platforms

1

While debugging some exception parameter update code in the constant potential implementation, I found a discrepancy between the extent that platforms check for modifications to exception parameters in `NonbondedForce.updateParametersInContext()`. Consider...

Constant potential simulations

1

We want to implement a method for [constant potential simulations](https://pubs.aip.org/jcp/article/126/8/084704/308896/Electrochemical-interface-between-an-ionic-liquid) of systems containing conductive electrodes in OpenMM. Existing implementations include that of the [ELECTRODE package](https://docs.lammps.org/fix_electrode.html) in LAMMPS, as well as...

Develop new OpenMM tutorials and update existing material

1

We discussed that the current experience for new users looking for tutorials to learn about how to use OpenMM is not ideal. The [pages in the user guide](http://docs.openmm.org/latest/userguide/application/02_running_sims.html) introducing how...

Constant potential tutorial

2

Adds a tutorial on setting up a constant potential simulation. Effectively shows how to replicate one data point from [this paper](https://doi.org/10.1063/5.0028232).

Equations in API documentation

1

Currently, information about the functional forms of energy terms, *etc.*, associated with various `Force`s is in the theory section of the user guide, while information about their APIs, and units...

SMIRNOFF: support virtual sites, multiple force field files

1

Adds support for SMIRNOFF virtual sites. Still draft quality; needs more testing for loading multiple OFFXML force field files simultaneously (this was necessary for some virtual site tests)

Validate Amber force fields against sander energies/forces

2

We discussed that it would be good to improve the validation done by the Amber force field conversion workflow. Currently, the "ground truth" against which results from the OpenMM FFXMLs...

Some CHARMM patches incorrectly apply to certain residues

1

I found a problem where the `PROP` (proline N-terminal) patch gets marked as applicable to some residues other than proline, which causes problems when they also allow the `NTER` (generic...