Allow SOMD1 pert file to be created without modifications to ghost atom bonded terms #407
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mb2055
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Jun 23, 2025
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This PR modifies the SOMD1 pert file writer to allow it to be written without modifications to ghost atom bonded terms. This enables the use of external modifications, e.g. those generated by the SOMD2
ghostlytool.The PR also includes a few fixes for running simulations of perturbable systems at the lambda = 1 end state and also when restraints are present.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]