A toy model of Friston's active inference in Tensorflow

Modular program for FEP/US calculations

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.

Hoomd plugin to apply a harmonic pinning potential on both translational and rotational motions.

NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms

Free energy from expanded ensemble simulations

Free energy from molecular dynamics simulations

C++ implementation of metadynamics simulation on a potential energy surface

A friendly Python library for multistate analysis with MICS and MBAR

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)

This repository is a bash script to prepare the simulation files for FreeEnergy calculation in GOMC.

Grand potential (Free energy) in finite temperature many-body perturbation theory

Programs for Information Topology Data Analysis

symbolic collective variable definitions and automation of metadynamics

A package for molecular dynamics analysis and parallel tempering in GROMACS

Python tutorial for estimating and clustering free energy landscapes with InfleCS.

The Valden Heat Pump controller is a platform to precisely control heat pumps

Open source toolkit for predicting bacterial porin permeation