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OpenFreeEnergy / openfe-gromacs

Gromacs-based protocols for Open Free Energy
https://openfe-gromacs.readthedocs.io/en/latest/
MIT License
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Example notebook for Gromacs MD simulations #22

Closed hannahbaumann closed 1 month ago

hannahbaumann commented 1 month ago

Description

This PR provides an example notebook for running MD simulations using openfe-gromacs.

Status

hannahbaumann commented 1 month ago

The creation of an Interchange object from_openmm and saving of the Interchange to .gro and .top files is still very slow (for solvated protein-ligand systems). In this example notebook it takes ~7min. Therefore the notebook is currently very slow.

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.41%. Comparing base (78840b2) to head (f9a4115). Report is 6 commits behind head on main.

Additional details and impacted files
IAlibay commented 1 month ago

The creation of an Interchange object from_openmm and saving of the Interchange to .gro and .top files is still very slow

Is this being tracked in an issue on the interchange repo? I feel like it might be off their radar.

IAlibay commented 1 month ago

@hannahbaumann with the fixes from #54 this should be a lgtm from me.