openmm/openmmforcefields: 0.12.0 Release
Creators
- 1. Memorial Sloan Kettering Cancer Center
- 2. @choderalab & @OpenFreeEnergy
- 3. Open Molecular Software Foundation
- 4. Chodera Lab // MSKCC
- 5. Stanford University
- 6. @rahko-ai
- 7. @cole-group
- 8. @openforcefield
Description
What's Changed Improvements
- Convert all amber ions (see https://github.com/openmm/openmm/issues/3663 for more detail) one-to-one using Amber ion frcmod files (from AmberTools 22) into OpenMM xml files with the same names and the same contents. by @mattwthompson & @aizvorski in https://github.com/openmm/openmmforcefields/pull/242 & https://github.com/openmm/openmmforcefields/pull/239
- SystemGenerator should only add barostat if system is periodic. Solves https://github.com/openmm/openmmforcefields/issues/252 by @jchodera in https://github.com/openmm/openmmforcefields/pull/253
- Fix OPC3 bond length. In the Amber implementation of the OPC3 water model at ffxml/amber/opc3.xml, the H-O bond length was too large by a factor of 10. by @mattwthompson in https://github.com/openmm/openmmforcefields/pull/273
- raise
ForceException
if a custom force is found. by @mattwthompson in https://github.com/openmm/openmmforcefields/pull/292
- Allow an offxml string to be used as a small molecule force field for the SystemGenerator and SMIRNOFFTemplateGenerator for example: ```python "Try and load a OFFXML string into a system generator object" from openmmforcefields.generators import SystemGenerator from openff.toolkit.typing.engines.smirnoff import ForceField from openff.toolkit.topology import Molecule import openmm
ff = ForceField("openff-2.0.0.offxml")
create a system generatorsystem_gen = SystemGenerator( forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml'], small_molecule_forcefield=ff.to_string() ) mol = Molecule.from_smiles("CC") system = system_gen.create_system(topology=mol.to_topology().to_openmm(), molecules=mol) with open("system.xml", "w") as output: output.write(openmm.XmlSerializer.serialize(system)) ``` by @jthorton in https://github.com/openmm/openmmforcefields/pull/288
- Support system and template generator for Espaloma 0.3. (espaloma 0.2. is no longer supported) by @ijpulidos in https://github.com/openmm/openmmforcefields/pull/293
- Bump codecov/codecov-action from 3.1.0 to 3.1.1 by @dependabot in https://github.com/openmm/openmmforcefields/pull/238
- Switch to
setup-micromamba
by @mattwthompson in https://github.com/openmm/openmmforcefields/pull/274 - Scattered fixes to get CI running by @mattwthompson in https://github.com/openmm/openmmforcefields/pull/290
- Update docstrings, run in CI by @mattwthompson in https://github.com/openmm/openmmforcefields/pull/240
- @jthorton made their first contribution in https://github.com/openmm/openmmforcefields/pull/288
Full Changelog: https://github.com/openmm/openmmforcefields/compare/0.11.2...0.12.0
Files
openmm/openmmforcefields-0.12.0.zip
Files
(31.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/openmm/openmmforcefields/tree/0.12.0 (URL)