Stephen Farr

Memory leak in NetCDF reporter

2

This is a duplicate of https://github.com/mdtraj/mdtraj/issues/1345 which is currently closed. It recently appeared again as an OpenMM issue: https://github.com/openmm/openmm/issues/4298 Using the mdtraj.NetCDFReporter causes eventual simulation slow down due to a...

torch.jit.script profile guided optimisations produce errors in aev_computer gradients

1

Hi, I have found that with pytorch 1.13 and 2.0 (not with pytorch

Different behavior on CPU vs CUDA platform when CustomNonbondedforce has no cutoff

8

This is from https://github.com/openmm/openmm-cookbook/issues/28 If you run the [Alchemical Free energy tutorial](https://openmm.github.io/openmm-cookbook/latest/notebooks/tutorials/Alchemical_free_energy_calculations.html) On the CUDA or OpenCL platform it will run. However, if you run it on the CPU platform...

torchscipt compatability for Ensemble

6

I could not make `Union[ Tuple[Tensor,Tensor], Tuple[Tensor,Tensor,Tensor,Tensor]]` work. It will jit.scipt but then if I try and use the model as energy,_ = model(..) it will complain: ``` RuntimeError: Union[Tuple[Tensor,...

There have been 3 new additions since the last release of the cookbook: bugfix in Alchemical free energy tutorial: #30 New CG polymer tutorial: #31 new cookbook example: #34

Turn off PR gh-actions deployment?

1

Currently when a PR is made a gh-actions workflow tries to build and deploy the PR onto the gh-pages branch so it can be viewed. However, this only works correctly...

The Colab notebooks are broken untilll this issue in condacolab is fixed: https://github.com/conda-incubator/condacolab/issues/60 Error you get when running in colab is: ``` No package can be installed for pin: cudatoolkit...

Adds a new basic tutorial for loading and parameterising a small molecule with OpenFF-toolkit and OpenMM-forceFields for use in OpenMM. From the workshop materials: https://github.com/openmm/openmm_workshop_july2023 cc @jmichel80 Rendered version can...

Adding ML examples

1

We should add cookboook examples that use OpenMM-ML, OpenMM-torch, and NNPOps. A potential problem with this is that adding PyTorch to the conda environment will make the Colab setup very...

Add support for NequIP models

22

This PR adds in support for NequIP models to openmm-ml. There are no pre-trained models available but the model framework is well defined. This will allow users to use their...