Frequently Asked Questions

I cannot install openmmtorchplugin

openmmtorchplugin depends on conda-forge builds of pyTorch and OpenMM. Due to this dependency, Windows cannot be supported.

Installation can be carried out via terminal with conda-forge:

conda install -c conda-forge openmmtorchplugin

The following Python versions are supported: 3.8, 3.9, 3.10, 3.11.

If you run into any issue, either at installation or runtime, ensure you have a plugin version >=1.1.3, as previous ones have known compatibility with OpenMM. The easiest way to ensure the most up to date version of molearn and the openmmtorchplugin are installed, is to run a fresh install in a new conda environment:

conda create --name test_env python=3.10
conda install -n test_env -c conda-forge openmmtorchplugin molearn

openmmtorchplugin is built with cuda_compiler_version=11.2 in conda-forge CI tools. This has been successfully tested on Ubuntu machines running with the driver version 525.105.17 (see nvidia-smi output).

The Nvidia website tabulates minimum driver versions required and version compatibility: NVIDIA CUDA Toolkit Minimum driver versions

I get an IndexError when I try loading a multiPDB

This is likely an error thrown by MDAnalysis. Typically this happens when attempting to load a multiPDB file saved with software like VMD, which uses a different syntax to indicate the end of a conformer in the file. A way to get around this, is to re-save the file in a format MDAnalysis can parse, e.g., by loading and re-saving the file via biobox.

import biobox as bb
M = bb.Molecule(filename)
M.write_pdb(newfilename)

The GUI freezes when I use it/does not work as expected

This is usually caused by an issue with packages handling communications between the GUI and Jupyter, see here. Currently, a workaround is to use older versions of tornado. In Python 3.10, the following packages have been observed to yield correct behaviour:

ipywidgets=8.0.7
nglview=3.0.6
tornado=6.1