shirtsgroup/cg_openmm
Tools to build coarse grained models and perform simulations with OpenMM
PythonMIT
Issues
- 0
Order of monomer bond lists in random builder
#153 opened by cwalker7 - 0
Update mbar code to work with pymbar 4.0
#151 opened by cwalker7 - 1
Update the stored cgmodel in the tests
#108 opened by cwalker7 - 1
Revisit binary interaction parameters
#111 opened by cwalker7 - 1
Fix imports for OpenMM 7.6
#133 opened by cwalker7 - 0
- 0
- 0
Add uncertainties in partial heat capacity function
#141 opened by cwalker7 - 0
Add example of heat capacity decomposition
#142 opened by cwalker7 - 0
Make heat capacity code more modular
#140 opened by cwalker7 - 0
Make the native contact symmetry checks more general
#143 opened by cwalker7 - 0
Using multiple reference simulations for reweighting
#139 opened by cwalker7 - 0
Revisit optimization / reweighting framework
#138 opened by cwalker7 - 0
- 0
- 2
Allow multiple angle styles in one system
#131 opened by cwalker7 - 0
Allow cgmodel monomers with no sidechains
#129 opened by cwalker7 - 1
Use openmm energies for helical modeling tool
#106 opened by cwalker7 - 2
fix test environment for python 3.8
#119 opened by cwalker7 - 2
Creating reweighting functionality
#71 opened by mrshirts - 0
modifying existing cgmodels
#117 opened by cwalker7 - 1
revisit the xml writer
#116 opened by cwalker7 - 0
add linting to CI
#115 opened by cwalker7 - 2
- 0
Support for non-standard mixing rules
#107 opened by cwalker7 - 1
- 1
Decide how we want to store analysis stats like decorrelation times and starting frame
#82 opened by cwalker7 - 3
process replica exchange running out of memory
#99 opened by cwalker7 - 2
rename equil_torsion_angle everywhere
#104 opened by cwalker7 - 0
list of quantities vs. quantity with list as value
#103 opened by cwalker7 - 3
Add tools for saving a molecular snapshot
#95 opened by cwalker7 - 0
- 0
- 2
Update documentation
#77 opened by cwalker7 - 4
Heat capacity calculation running out of memory
#79 opened by cwalker7 - 1
- 0
Allow for certain angle types to use 1-3 nonbonded interactions instead of harmonic angles
#87 opened by cwalker7 - 9
- 0
- 5
Negative weights for conformational state expectation in free energy calculation
#83 opened by cwalker7 - 1
- 2
Speeding up process_replica_exchange
#80 opened by cwalker7 - 0
- 0
- 0
- 2
- 1
- 0
- 0
physical validation tests failing with seg fault
#68 opened by cwalker7 - 1