Pinned Repositories
integrator-benchmark
Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318
neutromeratio
Tautomer ratios in solution
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
thresholds
Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318
advanced-ml-project
autoencoding for fun and profit
izhikevich-model
Simulate a small network of simple, diverse spiking neurons and analyze results
msm-learn
Learning how to learn Markov State Models of conformational dynamics
notebooks
Miscellaneous preliminary notebooks
bayes-implicit-solvent
experiments with Bayesian calibration of implicit solvent models
maxentile's Repositories
maxentile/izhikevich-model
Simulate a small network of simple, diverse spiking neurons and analyze results
maxentile/msm-learn
Learning how to learn Markov State Models of conformational dynamics
maxentile/notebooks
Miscellaneous preliminary notebooks
maxentile/ace
admission to candidacy exam
maxentile/automatic-state-decomposition
Automatic state decomposition Fortran90 code (outdated)
maxentile/bar-for-bayes-factors
[incomplete, buggy] using BAR+MBAR for model comparsion
maxentile/cellfree-expression
Tools for cell-free expression of proteins
maxentile/cgtools
Tools for developing coarse-graining schemes for Markov models
maxentile/equilibrium-sampling-tinker
experiments and tinkering with equilibrium sampling methods
maxentile/hugo-book
Hugo documentation theme as simple as plain book
maxentile/maxentile.github.io
maxentile/mbar-variants
small experimental variations on MBAR
maxentile/MBAR_ITIC
Merging the MBAR and ITIC methodologies to optimize a TraPPE force switch model
maxentile/mcmc-expectations
Tools for calculating expectations in a consistent way from MCMC samples
maxentile/mcmc_zoo
exploring the zoo of MCMC algorithms
maxentile/mdtraj
A modern, open library for the analysis of molecular dynamics trajectories
maxentile/method-of-moments-tinker
implementing / tinkering with method of moments estimators for multi-view models
maxentile/msm-pipeline
A pipeline for MSMs.
maxentile/msm-theory-sandbox
A playground for examples and tools to explore the theory of MSMs and related models.
maxentile/msmbuilder
Statistical models for biomolecular dynamics
maxentile/MSMs
Markov state models
maxentile/onion
Find TIS layers from MSM in dynamical systems
maxentile/onoma
generate silly names, then filter them using a markov model of word plausibility
maxentile/openmmtools
Test systems for OpenMM
maxentile/openpathsampling
An open source Python framework for transition interface and path sampling calculations.
maxentile/PyEMMA
Python API for Emma's Markov Model Algorithms
maxentile/radical.ensemblemd
The Radical Ensemble Molecular Dynamics (MD) Toolkit
maxentile/timemachine
Differentiate all the things!
maxentile/wivaprec
[work-in-progress] Find a change-of-variables that makes your MCMC problem easier
maxentile/yank
GPU-accelerated calculation of ligand binding affinities in implicit and explicit solvent using alchemical free energy methodologies