Pinned Repositories
addition-shirts-groupmeeting
A simple repo demonstrating the use of Travis CI and Readthedocs for the Shirts group meeting
alchemical-analysis
alchemlyb
the simple alchemistry library
article_templates
Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)
bayes1_manuscript
Manuscript for first paper on process using Bayesian inference to fully automate classical mechanics force field parameterization
cg_openmm
Tools to build coarse grained models and perform simulations with OpenMM
checkensemble
This software allows users to perform statistical test to determine if a given molecular simulation is consistent with the thermodynamic ensemble it is performed in.
conditional-flow-matching
Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport
CpHMD-Tutorial
Github repository for the LiveCoMS tutorial of the continuous constant pH molecular dynamics method
pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
mrshirts's Repositories
mrshirts/alchemlyb
the simple alchemistry library
mrshirts/pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
mrshirts/addition-shirts-groupmeeting
A simple repo demonstrating the use of Travis CI and Readthedocs for the Shirts group meeting
mrshirts/article_templates
Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)
mrshirts/bayes1_manuscript
Manuscript for first paper on process using Bayesian inference to fully automate classical mechanics force field parameterization
mrshirts/cg_openmm
Tools to build coarse grained models and perform simulations with OpenMM
mrshirts/conditional-flow-matching
Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport
mrshirts/CpHMD-Tutorial
Github repository for the LiveCoMS tutorial of the continuous constant pH molecular dynamics method
mrshirts/foldamers
Tools to model folding and evaluate thermodynamic properties for polymers and oligomers
mrshirts/gohugo-theme-ananke
Ananke: A theme for Hugo Sites
mrshirts/gromos_tutorial_livecoms
mrshirts/hugoBasicExample
Example site to use with Hugo & Hugo Themes
mrshirts/InterMol
Conversion tool for molecular simulations
mrshirts/JCED_FOMMS_Manuscript
mrshirts/journal_information
Information and documents supporting the work of the Living Journal of Computational Molecular Sciences (LiveCoMS)
mrshirts/lambda_MetaD_question
mrshirts/learned-replica-exchange
Skipping the replica exchange ladder with normalizing flows
mrshirts/livecomsjournal.github.io
GitHub Pages site for Living Journal of Computational Molecular Science
mrshirts/matlab-kinetic-modeling
mrshirts/MBAR_cyclohexane_test_bed
mrshirts/MBAR_ITIC
Merging the MBAR and ITIC methodologies to optimize a TraPPE force switch model
mrshirts/MBAR_LJ_two_states
mrshirts/MBAR_sampling_LJ_methane
This repository is designed to compare the MBAR results that are obtained for the Lennard-Jones representation of methane using configurations from 92 states and from just a single state.
mrshirts/open-forcefield-group.github.io
:triangular_ruler: A flexible two-column Jekyll theme. Perfect for personal sites, blogs, and portfolios hosted on GitHub or your own server.
mrshirts/OpenFF_Bilayer
mrshirts/ParmEd
Parameter/topology editor and molecular simulator
mrshirts/pymbar_reweight_example
Example for computing a reweighted PMF from MBAR
mrshirts/SAMPL6
Challenge inputs and details for the SAMPL6 challenge
mrshirts/tactile
Tactile is a Jekyll theme for GitHub Pages
mrshirts/UWDIRECT.github.io
Website for UW DIRECT classes, for program information see: http://www.cei.washington.edu/opportunities/direct/