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a-review-of-expanded-ensemble-methods

aiche_workshop_2017

2017 AICHE Hands On Molecular Simulation Workshop

alchemical_metadynamics_project

alchemistry.org

Source for alchemistry.org web page

alchemlyb

the simple alchemistry library

analyze_foldamers

Tools for structural analysis of coarse-grained foldamer simulations

basisanalyze

Tools to analyze basis function data from YANK simulations written with a special alchemy.py script.

bayes1_manuscript

Manuscript for first paper on process using Bayesian inference to fully automate classical mechanics force field parameterization

bcc_membrane

Build bicontinuous cubic structure

cg_openmm

Tools to build coarse grained models and perform simulations with OpenMM

cg_pyrosetta

A python package which enables CG residues in a working version of PyRosetta

charge_correction

Correction scheme for electrostatic finite-size effects

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.

computational_training

Resources for computational training

droplet-analysis

Tools for building and analyzing nanoscale droplets.

ensemble_md

A python package for performing GROMACS simulation ensembles

eyring_model

finite-temperature-crystal-scripts

Useful scripts to add finite temperature effects

foldamers

Tools to model folding and evaluate thermodynamic properties for polymers and oligomers

glycoinsulin_analysis

A python package for assessing the proteolytic stability and dimerization propensity of O-glycosylated insulin

gromacs_wlmod

Modifications for wang-landau

hdphmm

A Bayesian classifier for detecting and parameterizing an unknown number of latent states.

intermol

Conversion tool for molecular simulations

ion-parameters

This houses the main scripts I use for creating the iterative ion parametrization.

lattice_dynamics

llc_cg_build

llc_membranes

Set up, simulate and analyze the results of molecular dynamics simulations of lyotropic liquid crystal membranes

llcsim

Set up molecular dynamics simulations of lyotropic liquid crystal membranes, and analyze the resulting trajectories

mbar_mixtures

A short paper on MBAR interpreted as reweighting from the mixtures distribution

mbar_presentation_2_20_19

Files and examples related to MBAR presentation for the Shirts group by Lenny, Wei-Tse, and Garrett on 2/20/19