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Document new efpmd options, fragment frame and label formats - #31
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efpmd.rst: ligand_cutoff (and how cutoffs are measured), pairwise_ligand_only, print_pairwise_geometry, print_geometry, TIMING lines of print 1, etest without gradients; corrected default of ligand (-100, no ligand). parameters.rst: LibEFP moves fragments to their center-of-mass frame (any frame can be used in the .efp file; xyzabc positions and cutoffs refer to the center of mass; MD needs principal axes); name tags as 8-character fields and bond midpoints of fragments with more than 99 atoms (no renaming needed); CT tags of polarizable points, dynamic polarizable points and LMO centroids. These describe the changes in libefp branch lyuda_bugfix_Oct2026. Co-Authored-By: Claude Opus 5.5 <[email protected]>
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Documents the changes in libefp branch lyuda_bugfix_Oct2026.
efpmd.rst
ligand_cutoff: separate cutoff for all pairs with the ligand; note that cutoffs are measured between fragment centers of masspairwise_ligand_only: two-body terms only for the pairs with the ligand (polarization of the whole system as usual)print_pairwise_geometry,print_geometry: shorter output for large systemsprint 1now also prints TIMING lines of the main phasesetestcomputes the energy without gradientsligand(-100, no ligand; -1 = QM region)parameters.rst
xyzabcand cutoffs refer to the center of mass; MD needs principal axesChecked with the workflow's packages (sphinx, sphinx_rtd_theme, myst_parser, sphinx_panels): no new warnings.
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