Free energy from expanded ensemble simulations
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Updated
Nov 28, 2018 - Python
Free energy from expanded ensemble simulations
Hoomd plugin to apply a harmonic pinning potential on both translational and rotational motions.
Protein folding with local propensity using GA
Application of active inference to reinforcement learning.
Modular program for FEP/US calculations
Free energy from molecular dynamics simulations
symbolic collective variable definitions and automation of metadynamics
Open source toolkit for predicting bacterial porin permeation
C++ implementation of metadynamics simulation on a potential energy surface
Official implementation of article "Including explicitly treated interfacial water molecules improved the free energy calculation for the binding of SARS-CoV-2 spike RBD and antibodies".
This repository is a bash script to prepare the simulation files for FreeEnergy calculation in GOMC.
Python tutorial for estimating and clustering free energy landscapes with InfleCS.
Grand potential (Free energy) in finite temperature many-body perturbation theory
Extended Phase-Space Simulations with OpenMM
Software to Assess Association Free Energies via Direct Estimative of Partition Functions
Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)
Path of least action analysis on energy landscapes
Permutationally invariant networks for enhanced sampling (PINES)
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.
Software implementation for paper Heuristic Analysis of Manifolds from Simulated Cryo-EM Ensemble Data
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