🚂 Python API for Emma's Markov Model Algorithms 🚂
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.
Construction of windows based on free energy. This module has the "cowboe" algorithm which can be used for parameter selection with umbrella sampling.
Functional prototype of a web platform for Molecular Dynamics (MD) and Monte Carlo (MC) simulations oriented to computational physics, theoretical chemistry and materials science.
Free energy from molecular dynamics simulations
Modular program for FEP/US calculations
Reproducible GROMACS workflow for umbrella sampling, PMF calculation, and free-energy analysis.
Monte Carlo package for simulating atoms interacting with non-bonded potentials
tools for molecular dynamics: docking, metadynamics, umbrella sampling, high-throughput screening, etc.
Processed-data reproducibility package for ST-eUS/WHAM/Hummer/ISD analysis of CNFD passive permeation across a model lipid bilayer.
Simulation of block copolymer escape dynamics using a bead-spring model with Monte Carlo and forward-flux sampling. Includes free-energy profiling via umbrella sampling and escape rate estimation from micelle cores.
To associate your repository with the umbrella-sampling topic, visit your repo's landing page and select "manage topics."