Code

Fix AMBER FEP mappings#366

Code

Merged

lohedges merged 15 commits intodevelOpenBioSim/biosimspace:develfrom fix_amber_fep_mappingsOpenBioSim/biosimspace:fix_amber_fep_mappingsCopy head branch name to clipboardNov 25, 2024

+429-122

Commits

Commits on Nov 13, 2024

• Add functionality to prune mappings for use with AMBER.

  lohedges

  committed
  76ae572

  Copy full SHA for 76ae572

• Apply FEP analysis pre-processing modifications.

  lohedges

  committed
  7e1c763

  Copy full SHA for 7e1c763

• AMBER only supports the full FEP perturbation type.

  lohedges

  committed
  422a549

  Copy full SHA for 422a549

• Update GROMACS configuration settings.

  lohedges

  committed
  8b8e0db

  Copy full SHA for 8b8e0db

Commits on Nov 14, 2024

• Simplify reporting of FEP energies and gradients.

  lohedges

  committed
  631dcb6

  Copy full SHA for 631dcb6

• Make defaults consistent across protocols.

  lohedges

  committed
  2600aeb

  Copy full SHA for 2600aeb

• No longer need to set report and restart interval in test.

  lohedges

  committed
  1e34318

  Copy full SHA for 1e34318

• Optimise SOMD settings.

  lohedges

  committed
  976ab36

  Copy full SHA for 976ab36

• Update AMBER reference values following analysis tweaks.

  lohedges

  committed
  373876c

  Copy full SHA for 373876c

• Fix maximum trajectory index.

  lohedges

  committed
  e017148

  Copy full SHA for e017148

Commits on Nov 15, 2024

• Add functionality to prune changing atom types from mapping.

  lohedges

  committed
  f7e8208

  Copy full SHA for f7e8208

• Add restart flag to equilibration protocols.

  lohedges

  committed
  26bd4ec

  Copy full SHA for 26bd4ec

• Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

  lohedges

  committed
  9bce525

  Copy full SHA for 9bce525

• Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

  lohedges

  committed
  870c175

  Copy full SHA for 870c175

Commits on Nov 18, 2024

• Merge branch 'devel' into fix_amber_fep_mappings [ci skip]

  lohedges

  committed
  78444b6

  Copy full SHA for 78444b6