Example notebook for Gromacs MD simulations #22
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The creation of an Interchange object |
Closed
Is this being tracked in an issue on the interchange repo? I feel like it might be off their radar. |
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@hannahbaumann with the fixes from #54 this should be a lgtm from me. |
* Remove OpenMMEngineSettings * Update token * Small fix * Removes output files from results if they should not exist * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Forgot to enable tests again * Remove stub files * Update results file * Have MDPs be a dictionary rather than a list of file handles * Move vacuuum disallowed check to Protocol creation * Update token * Add interchange environment variable to protocol * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update openfe_gromacs/protocols/gromacs_md/md_methods.py Co-authored-by: Irfan Alibay <[email protected]> * Address review comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add GromacsEngineSettings * Add defaults, validator * Rename to GromacsEngineSettings * Update test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update openfe_gromacs/protocols/gromacs_md/md_methods.py Co-authored-by: Irfan Alibay <[email protected]> * Update tokens * Update docstring in ProtocolResults * Update tests * Update openfe_gromacs/protocols/gromacs_md/md_methods.py Co-authored-by: Irfan Alibay <[email protected]> * Update openfe_gromacs/protocols/gromacs_md/md_methods.py Co-authored-by: Irfan Alibay <[email protected]> * Update openfe_gromacs/protocols/gromacs_md/md_methods.py Co-authored-by: Irfan Alibay <[email protected]> * various things * more changes to the notebook * Add docs building * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move sass.py over * Add _ext folder * fix up docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix docs * Add example notebook to the docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add pathlib import * Fix title underline * Fix the title * Update warning * fix a few things --------- Co-authored-by: hannahbaumann <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Baumann <[email protected]>
IAlibay
approved these changes
Sep 30, 2024
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Description
This PR provides an example notebook for running MD simulations using openfe-gromacs.
Status