Add support for writing energy components to file and preserving the LJ sigma parameter for ghost atoms #44
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mb2055
previously approved these changes
May 28, 2024
fixed a typo in the installation instructions
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I've updated this to match the logic from Sire, i.e. all zero sigmas are set to the opposite end state value, not just those for ghost atoms. I've also included a fix for @jmichel80's issue, where it isn't possible to create a system from a perturbation template when the free system only included the ligand and water. This makes sure that the search returns a |
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This PR adds support for writing the energy components (from each force) to a log file for debugging purposes with the
--save-energy-componentscommand-line option. This also builds on OpenBioSim/sire#198 and OpenBioSim/biosimspace#295 to prevent perturbation of the LJ sigma parameter for ghost atoms, which causes instability during perturbation.