shirtsgroup/cg_openmm issues and pull requests

#155 - pymbar 4 update

Pull Request - State: open - Opened by cwalker7 almost 2 years ago

#154 - Update helix optimization tools

Pull Request - State: open - Opened by cwalker7 about 2 years ago - 1 comment

#153 - Order of monomer bond lists in random builder

Issue - State: open - Opened by cwalker7 about 2 years ago

#152 - Anisotropic potentials and Go model tools

Pull Request - State: closed - Opened by cwalker7 about 2 years ago - 1 comment

#151 - Update mbar code to work with pymbar 4.0

Issue - State: open - Opened by cwalker7 about 2 years ago

#150 - Mie potentials with binary interaction parameter mixing rules

Issue - State: open - Opened by cwalker7 over 2 years ago

#149 - Helix geometry modeling for 2 and 3 sidechain models

Pull Request - State: closed - Opened by cwalker7 over 2 years ago

#148 - Mie potentials and updated binary interaction parameter scheme

Pull Request - State: closed - Opened by cwalker7 over 2 years ago - 1 comment

#147 - Fix configurational state heat capacities for low population fractions

Issue - State: open - Opened by cwalker7 over 2 years ago

#146 - Update OpenMM imports

Pull Request - State: closed - Opened by cwalker7 over 2 years ago - 1 comment

#145 - Custom nonbonded exclusion rules

Pull Request - State: closed - Opened by cwalker7 over 2 years ago - 3 comments

#144 - Energy decomposition function, native contacts by configurational state

Pull Request - State: open - Opened by cwalker7 over 2 years ago - 1 comment

#143 - Make the native contact symmetry checks more general

Issue - State: open - Opened by cwalker7 almost 3 years ago
Labels: enhancement

#142 - Add example of heat capacity decomposition

Issue - State: open - Opened by cwalker7 almost 3 years ago
Labels: knots paper

#141 - Add uncertainties in partial heat capacity function

Issue - State: open - Opened by cwalker7 almost 3 years ago
Labels: knots paper

#140 - Make heat capacity code more modular

Issue - State: open - Opened by cwalker7 almost 3 years ago
Labels: enhancement

#139 - Using multiple reference simulations for reweighting

Issue - State: open - Opened by cwalker7 almost 3 years ago

#138 - Revisit optimization / reweighting framework

Issue - State: open - Opened by cwalker7 almost 3 years ago

#137 - Multiple folded state capability

Pull Request - State: closed - Opened by cwalker7 almost 3 years ago - 2 comments

#136 - Implement energy scan for local angle/torsion stiffness

Issue - State: open - Opened by cwalker7 about 3 years ago

#135 - Sequence optimization update, fix native distances bug

Pull Request - State: closed - Opened by cwalker7 about 3 years ago

#134 - Implement more general angle and torsion types for heteropolymers

Issue - State: open - Opened by cwalker7 about 3 years ago
Labels: enhancement

#133 - Fix imports for OpenMM 7.6

Issue - State: closed - Opened by cwalker7 about 3 years ago - 1 comment
Labels: For release

#132 - function for binary sequence FWHM eval

Pull Request - State: closed - Opened by cwalker7 about 3 years ago - 6 comments

#131 - Allow multiple angle styles in one system

Issue - State: open - Opened by cwalker7 about 3 years ago - 2 comments
Labels: enhancement

#130 - 1d general native contact cutoff optimization

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#129 - Allow cgmodel monomers with no sidechains

Issue - State: open - Opened by cwalker7 over 3 years ago

#128 - Restarting / extending replica exchange simulations

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 2 comments

#127 - dcd support for single temp MD

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#126 - Configurational sampling with non-simulated force field parameters

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 6 comments

#125 - Use MDTraj trajectory writing tools

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 2 comments

#124 - fix documentation links to functions

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#123 - Update documentation and add examples

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#122 - Helix optimization with openmm energies

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 2 comments

#121 - Restricted bending angle potential

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 3 comments

#120 - examples for cg_openmm paper

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#119 - fix test environment for python 3.8

Issue - State: closed - Opened by cwalker7 over 3 years ago - 2 comments

#118 - update helical native contacts for short chains

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#117 - modifying existing cgmodels

Issue - State: open - Opened by cwalker7 over 3 years ago

#116 - revisit the xml writer

Issue - State: open - Opened by cwalker7 over 3 years ago - 1 comment
Labels: For release

#115 - add linting to CI

Issue - State: open - Opened by cwalker7 over 3 years ago
Labels: For release

#114 - update docstrings in secondary structure

Pull Request - State: closed - Opened by cwalker7 over 3 years ago

#113 - Heat capacity bootstrapping

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 1 comment

#112 - Native contacts optimization and signac project scripts

Pull Request - State: closed - Opened by cwalker7 over 3 years ago - 2 comments

#111 - Revisit binary interaction parameters

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 1 comment
Labels: Future

#110 - Replica exchange transition analysis 12_30_20

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 4 comments

#109 - Binary interaction parameters

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 2 comments

#108 - Update the stored cgmodel in the tests

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 1 comment

#107 - Support for non-standard mixing rules

Issue - State: open - Opened by cwalker7 almost 4 years ago

#106 - Use openmm energies for helical modeling tool

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 1 comment
Labels: Future

#105 - Helical modeling

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 2 comments

#104 - rename equil_torsion_angle everywhere

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 2 comments
Labels: For release

#103 - list of quantities vs. quantity with list as value

Issue - State: open - Opened by cwalker7 almost 4 years ago
Labels: Discussion

#102 - Sums of periodic torsions

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 2 comments

#101 - fixing units in process replica exchange

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago

#100 - Use Yank code's method for trajectory writing

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 2 comments

#99 - process replica exchange running out of memory

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 3 comments

#98 - Optimize native contacts

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 1 comment

#97 - Add function for restarting a replica exchange simulation

Issue - State: open - Opened by cwalker7 almost 4 years ago
Labels: enhancement

#96 - updating signac scripts

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago

#95 - Add tools for saving a molecular snapshot

Issue - State: closed - Opened by cwalker7 almost 4 years ago - 3 comments
Labels: enhancement

#94 - Update docs for cgmodel

Pull Request - State: closed - Opened by cwalker7 almost 4 years ago - 1 comment

#93 - Add option to suppress openmmtools and pymbar warnings

Issue - State: open - Opened by cwalker7 almost 4 years ago
Labels: For release

#92 - adding readthedocs conda environment

Pull Request - State: closed - Opened by cwalker7 about 4 years ago

#91 - Miscellaneous updates 11_2_20

Pull Request - State: closed - Opened by cwalker7 about 4 years ago

#90 - update heat capacity function to get temperature list from .nc file

Issue - State: closed - Opened by cwalker7 about 4 years ago - 1 comment
Labels: For release

#89 - adding physical validation test files

Pull Request - State: closed - Opened by cwalker7 about 4 years ago

#88 - Bootstrapping code for free energy / entropy / enthalpy of folding

Pull Request - State: closed - Opened by cwalker7 about 4 years ago

#87 - Allow for certain angle types to use 1-3 nonbonded interactions instead of harmonic angles

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: enhancement

#86 - Deal with energy spikes while maintaining large time step

Issue - State: open - Opened by cwalker7 about 4 years ago - 9 comments

#85 - Remove extra loop in calculating average energies.

Issue - State: open - Opened by mrshirts about 4 years ago
Labels: Future

#84 - Signac workflows and sigmoid fitting

Pull Request - State: closed - Opened by cwalker7 about 4 years ago - 3 comments

#83 - Negative weights for conformational state expectation in free energy calculation

Issue - State: open - Opened by cwalker7 about 4 years ago - 5 comments

#82 - Decide how we want to store analysis stats like decorrelation times and starting frame

Issue - State: closed - Opened by cwalker7 about 4 years ago - 1 comment
Labels: For release

#81 - Native contacts dcd

Pull Request - State: closed - Opened by cwalker7 about 4 years ago - 4 comments

#80 - Speeding up process_replica_exchange

Issue - State: open - Opened by cwalker7 about 4 years ago - 2 comments
Labels: enhancement

#79 - Heat capacity calculation running out of memory

Issue - State: closed - Opened by cwalker7 about 4 years ago - 4 comments
Labels: For release

#78 - Verify the uncertainty calculation of free energy of folding

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: For release

#77 - Update documentation

Issue - State: open - Opened by cwalker7 about 4 years ago - 2 comments
Labels: For release

#76 - Reorganize utilities and consider renaming the modules

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: For release

#75 - Decide what we want to do with ens_build.py and ensemble library

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: For release

#74 - replica exchange energy pdf plots load very slowly

Issue - State: closed - Opened by cwalker7 about 4 years ago - 2 comments
Labels: For release

#73 - Implement either periodic torsions or RB torsions

Issue - State: closed - Opened by mrshirts about 4 years ago - 1 comment
Labels: For release

#72 - How to do enthalpy/entropy of configurational states

Issue - State: open - Opened by mrshirts about 4 years ago - 1 comment

#71 - Creating reweighting functionality

Issue - State: open - Opened by mrshirts about 4 years ago - 2 comments
Labels: For release

#70 - Updating expectation_native_contacts

Pull Request - State: closed - Opened by cwalker7 about 4 years ago - 7 comments

#69 - precision of positions stored in .nc file vs. pdb files

Issue - State: open - Opened by cwalker7 about 4 years ago - 2 comments
Labels: Discussion

#68 - physical validation tests failing with seg fault

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: For release

#67 - Detect equilibration and select frames for analysis

Pull Request - State: closed - Opened by cwalker7 about 4 years ago - 1 comment

#66 - Units issue in the distance() function in random_builder.py

Issue - State: open - Opened by cwalker7 about 4 years ago - 1 comment
Labels: For release

#65 - add ability to select frames for thermodynamic analysis

Issue - State: open - Opened by cwalker7 about 4 years ago
Labels: For release

#64 - replace distance calculations with mdtraj

Issue - State: open - Opened by cwalker7 over 4 years ago - 3 comments
Labels: Future

#62 - duplicate element error when making multiple cgmodels

Issue - State: closed - Opened by cwalker7 about 4 years ago - 1 comment

#61 - free energy code for conformational state changes

Pull Request - State: closed - Opened by cwalker7 about 4 years ago - 14 comments

#54 - Considering combining calc_temperature_spacing and get_temperature_list functions

Issue - State: closed - Opened by cwalker7 over 4 years ago - 2 comments
Labels: enhancement

#53 - Torsions as sums of periodic terms

Issue - State: closed - Opened by mrshirts over 4 years ago - 5 comments
Labels: For release

#51 - Get random builder working with include_torsion_forces=True

Issue - State: open - Opened by cwalker7 over 4 years ago - 1 comment
Labels: For release

#46 - Ensemble physical validation crashes when temperature pairs set to 'all'

Issue - State: closed - Opened by cwalker7 over 4 years ago - 1 comment
Labels: For release

#45 - Update all examples to use the new cgmodel monomer input

Issue - State: closed - Opened by cwalker7 over 4 years ago - 1 comment
Labels: For release

#29 - Investigate use of timeseries module from pymbar for expectations calculations

Issue - State: closed - Opened by mrshirts over 4 years ago - 1 comment

GitHub / shirtsgroup/cg_openmm issues and pull requests