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Fix AMBER FEP mappings #366

Merged
merged 15 commits into from
Nov 25, 2024
Merged

Fix AMBER FEP mappings #366

merged 15 commits into from
Nov 25, 2024

Commits on Nov 13, 2024

  1. Add functionality to prune mappings for use with AMBER.

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    lohedges committed Nov 13, 2024
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  2. Apply FEP analysis pre-processing modifications.

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    lohedges committed Nov 13, 2024
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  3. AMBER only supports the full FEP perturbation type.

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    lohedges committed Nov 13, 2024
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  4. Update GROMACS configuration settings.

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    lohedges committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. Simplify reporting of FEP energies and gradients.

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    lohedges committed Nov 14, 2024
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  2. Make defaults consistent across protocols.

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    lohedges committed Nov 14, 2024
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  3. No longer need to set report and restart interval in test.

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    lohedges committed Nov 14, 2024
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  4. Optimise SOMD settings.

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    lohedges committed Nov 14, 2024
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  5. Update AMBER reference values following analysis tweaks.

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    lohedges committed Nov 14, 2024
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  6. Fix maximum trajectory index.

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    lohedges committed Nov 14, 2024
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Commits on Nov 15, 2024

  1. Add functionality to prune changing atom types from mapping.

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    lohedges committed Nov 15, 2024
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  2. Add restart flag to equilibration protocols.

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    lohedges committed Nov 15, 2024
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  3. Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

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    lohedges committed Nov 15, 2024
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  4. Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

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    lohedges committed Nov 15, 2024
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Commits on Nov 18, 2024

  1. Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

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    lohedges committed Nov 18, 2024
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