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choderalab/yank: YANK 0.14.1: Early Access 1.0 Release

Authors: John Chodera; Andrea Rizzi; Levi Naden; Kyle Beauchamp; Patrick Grinaway; Bas Rustenburg; Steven Albanese;

choderalab/yank: YANK 0.14.1: Early Access 1.0 Release

Abstract

This release marks the early access phase for YANK 1.0. We intend for this to be a formal release for users to test YANK and its functionality while we refactor the underlying Python API. In this release: YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0 New features may appear in the time meantime, but scripts will be forwards compatible. Initial support for OpenMM XML systems and PDB files Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files clearance in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline Boresch Orientational Restraints fully implemented and documented. Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg Documentation updated with better algorithms and theory sections. Full walkthroughs of yank-examples added to online documentation Various other documentation improvements Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1) YANK now on MIT License Many bugfixes

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average