Iván Pulido

Adding Fossil SCM support to spaceship prompt

1

This pull request adds [Fossil SCM](https://www.fossil-scm.org/) to Spaceship Prompt. It's as light and fast as the others (mercurial and git), since it follows the same logic/structure. I chose an alchemical...

Streamlined building instructions using `conda-forge` packages

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From the experience captured in #3721, I noted that there can be some unexpected issues when we create a build environment using the [current instructions ](https://github.com/openmm/openmm/blob/master/docs-source/usersguide/library/02_compiling.rst). Specifically, when we do...

Openmm failing with cudatoolkit>=11.6

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I have seen openmm failing with the following message `CUDA platform error: Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) ` when using it in a conda environment with `cudatoolkit=11.6`. To reproduce...

Canonical order before conformer generation

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Fixes #926 - [x] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/master/openff/toolkit/tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/master/docs), if applicable - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase - [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/master/docs/releasehistory.rst)

Topology molecules without topology

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**Describe the bug** I create a new topology molecule specifying its topology and the specified topology does not have the topology molecule as part of its topology molecules. Should there...

Avoid raising broad `Exception` when raising errors

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Some check and errors are raised with generic `Exception` objects, this can lead to some troubles in the future even if we are safe now. We should enhance our code...

We want to port the notebook analysis and analyzer objects to `openmmtools`. CC https://github.com/choderalab/yank/issues/1282

Resuming and basic tests with MPI context

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While working on #602 it was noted that the issue is only relevant when the simulations are run using 2 or more MPI processes (multiple GPUs). Therefore, we need a...

Renaming (or aliasing?) `online_analysis_interval`

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Note that we may also want to consider opening an issue for renaming `self.online_analysis_interval` to `self.offline_analysis_interval` _Originally posted by @zhang-ivy in https://github.com/choderalab/openmmtools/issues/592#issuecomment-1149053115_

From working in #593 it was noted that we need better testing for the offline analysis and MBAR estimates that end up in the real time analysis file.