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