########################## Frequently Asked Questions ########################## 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. .. code-block:: import biobox as bb M = bb.Molecule(filename) M.write_pdb(newfilename) 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: .. code:: conda install -c conda-forge openmmtorchplugin The following Python versions are supported: 3.8, 3.9, 3.10, 3.11. If you are running into any issue, attempt a fresh install in a new conda environment: .. code:: conda create --name test_env python=3.10 conda install -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 `_ 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: .. code:: ipywidgets=8.0.7 nglview=3.0.6 tornado=6.1