John's repositories
adaptivemd
A python framework to run adaptive Molecular Dynamics simulations using Markov State Modelling on HPC resources
admdrpruns
Files to install and run AdaptiveMD with Radical Pilot execution manager.
adaptivemd-summit
Changes to AdaptiveMD specific to OLCF Summit
admdgenerator
Scripts for AdaptiveMD workflow creation and runtime operations
admdinstaller
Installer script for AdaptiveMD providing platform and configuration.
aswa-usecase
Setup for using ASWAnalysis
aswanalysis
Analyze Adaptive Sampling Workflow Results
chignolin-workflows
AdaptiveMD workflows for the chignolin system
compare-ltj-asw
Compare long trajectory with adaptive sampling workflow
mdtraj-nogeo
MDTraj Formats for use on non-x86 architectures
mergegrids
Merge voxel properties from statistical replicates of data stored in UHBD grid format
msmworkshop
Jupyter Notebooks and sample data for MSM creation pipeline and plots along the way.
test-workflows
Files for testing adaptivemd workflows
tests-suite
HPC Tests for Radical Pilot, OpenMM, and AdaptiveMD
timetimer
Create a "Storyline" of parallel program execution timelines, via a set of output files with timestamps.
workflow-analysis
Process AdaptiveMD workflow timestamps
xyztraj
Read and work with XYZ trajectory files sans-topology