Pinned Repositories
alchemical-protein-ligand
Scripts to perform alchemical ABFE in OpenMM
CppND-Capstone-Ising
My Udacity C++-NanoDegree Capstone project
funnel_potential
Implementation of the funnel potential in NAMD and OpenMM
hfe-openmm-jupyter
This repository contains jupyter notebooks to calculate hydration free energies in OpenMM
HG-GBSA-Optimization
Example for running GBSA optimization targeting host-guest binding data with OpenFF-Evaluator and ForceBalance
ion_solvation_openmm
Ion solvation free energy with spherical boundary conditions
pAPRika
Advanced toolkit for binding free energy calculations
position_diffusion
Position dependent diffusivity of a molecule that is under an external harmonic potential
random-scripts
A collection of useful scripts (pre- and post-processing) because I keep forgetting where I kept them
Udacity-Deep-Learning-Nanodegree
This repository contains my project submission to the deep learning nanodegree from Udacity
jeff231li's Repositories
jeff231li/ion_solvation_openmm
Ion solvation free energy with spherical boundary conditions
jeff231li/funnel_potential
Implementation of the funnel potential in NAMD and OpenMM
jeff231li/random-scripts
A collection of useful scripts (pre- and post-processing) because I keep forgetting where I kept them
jeff231li/alchemical-protein-ligand
Scripts to perform alchemical ABFE in OpenMM
jeff231li/hfe-openmm-jupyter
This repository contains jupyter notebooks to calculate hydration free energies in OpenMM
jeff231li/HG-GBSA-Optimization
Example for running GBSA optimization targeting host-guest binding data with OpenFF-Evaluator and ForceBalance
jeff231li/osmotic_pressure_openmm
Calculate the osmotic pressure of NaCl using the OpenMM simulation engine
jeff231li/pAPRika
Advanced toolkit for binding free energy calculations
jeff231li/Udacity-Deep-Learning-Nanodegree
This repository contains my project submission to the deep learning nanodegree from Udacity
jeff231li/adamantanes-temperature-scripts
Repository containing setup and analysis scripts used in the paper studying the temperature-dependence of adamantanes host-guest binding.
jeff231li/alchemical-relative-solvation
NAMD files for performing relative solvation free energy
jeff231li/cpptraj
Biomolecular simulation trajectory/data analysis.
jeff231li/forcebalance
Systematic force field optimization.
jeff231li/FreeSolv
Experimental and calculated small molecule hydration free energies
jeff231li/gisttools
Post-processing of data generated by the GIST (Grid Inhomogeneous Solvation Theory) action in cpptraj
jeff231li/growing_dummy_particle
OpenMM files for growing a dummy atom in a host cavity
jeff231li/host-guest-benchmarks
Host-guest structures for binding free energy benchmarks
jeff231li/mars
jeff231li/MDRestraintsGenerator
Python code for generating Boresch restraints from MD simulations
jeff231li/molecular_shrink_ray
jeff231li/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
jeff231li/openff-evaluator
A physical property evaluation toolkit from the Open Forcefield Consortium.
jeff231li/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
jeff231li/paprika-feedstock
A conda-smithy repository for paprika.
jeff231li/paprika-taproom-scripts
Repository that contains scripts to generate APR files from Taproom repository in pAPRika
jeff231li/pseudo-hard-sphere-solvation-scripts
Repository containing setup and analysis scripts used in the paper investigating "high-energy" water in cucurbit[n]uril.
jeff231li/SAMPL7-Scripts
Scripts I used to generate and run SAMPL7 host-guest systems
jeff231li/SAMPL9-bCD
A place where to share SAMPL9 bCD challenge input files etc.
jeff231li/SAMPLing
jeff231li/Udacity-Deep-Reinforcement-Learning-Projects
Project submission for the Udacity Deep RL nanodegree