mosdef-hub / gmso

Flexible storage of chemical topology for molecular simulation

https://gmso.mosdef.org

mosdef-hub/gmso Issues

Dihedral Improper sorting not compatible with (via mosdef-GOMC) NAMD
Closed 6 months ago4
Priority when parameterizing connection is flipped
Closed 6 months ago
Issue with Molecule numbering
Closed 6 months ago2
JSON handling for parameterized topologies
Closed 7 months ago5
Bug with GRO reader
Closed 7 months ago
Bug in Elementary charges in json loading
Closed 7 months ago2
Tests failing with `unyt 3.0`
Closed 8 months ago
Error when writing/converting foyer to gmso xml files
Updated 9 months ago2
Loading for XMLS bug
Closed 9 months ago4
Foyer to GMSO converter does not work for periodic dihedral types
Updated 9 months ago3
Daily CI failing
Closed 9 months ago
Multiple Dihedral types (equations) not accepted (Example: CHARMM style with Periodic and Harmonic dihedrals)
Closed 9 months ago3
Issue with parsing impropers in `to_hoomd_forcefield` using GAFF xml
Closed 9 months ago2
Potential Issue with GROMACS gro writer
Updated 10 months ago
Module gmso.core.unit_systems
Closed 10 months ago1
Unyt 2.9.3 break stuff
Closed 10 months ago1
Numpy 1.25.0 will no longer support comparison to string
Closed 10 months ago3
HOOMD snapshot and to HOOMD Forcefield discrepancy
Closed 10 months ago
Performance issue with `to_parmed`
Closed 10 months ago1
HOOMD Forcefield compatibility issues
Updated 10 months ago
Use `forcefield-utilities` to load a GMSO xml file
Closed a year ago1
Is there a way to remove sites from a topology?
Closed a year ago3
Use Forcefield utilities for all backend loading
Closed a year ago
Performance significantly affected by "flatness" of the compounds
Closed a year ago6
Unit conversions in packages should be added to utils.units
Closed a year ago
Issue with writing virtual sites via a lone pair
Updated a year ago3
New Pydantic release breaks thing (again)
Closed a year ago
New pydantic release has breaking changes
Closed a year ago
Unpin HOOMD
Closed a year ago
Going back and forth between ParmEd and and GMSO raises issues
Closed a year ago1
Breaking changes in gsd 3.0
Closed a year ago3
Update Github actions
Closed a year ago
Issue in conversion from parmed
Closed a year ago
Add support to write out rigid water for GROMACS
Updated a year ago1
Performance issue when converting typed topology to parmed
Closed a year ago2
AttributeError from `base_units` in `to_hoomd_forcefield` method
Closed a year ago2
GROMACS pairs edge case
Closed a year ago
Gromacs writer truncates residue and atom type names too short.
Closed a year ago2
Bug in Topology Iter sites
Closed a year ago
gmso FF periodic dihedrals and impropers yield a unyt_quantity or unyt_array
Updated 2 years ago
Allow multiple set of scaling factors and mixing rule
Closed 2 years ago
Convert from mBuild better warning messages
Closed 2 years ago
Account for mass in convert_mbuild.py
Closed 2 years ago1
Unyt Issues
Closed 2 years ago2
account for charges in `convert_mbuild.py`
Closed 2 years ago11
`write_gsd` doesn't work when no mass is set
Closed 2 years ago10
About automating consolidation of parameters while using GMSO ForceField XML.
Updated 2 years ago
Discussion on long term changes for GMSO-MoSDeF workflows
Updated 2 years ago
Add Expected Dimensions for PotentialTemplate parameters.
Closed 2 years ago1
RuntimeError: "unyt_quantity instances must be scalars" while cloning potentials
Closed 2 years ago1