umbrella-sampling

🚂 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.

Modular program for FEP/US calculations

Free energy from molecular dynamics simulations

Functional prototype of a web platform for Molecular Dynamics (MD) and Monte Carlo (MC) simulations oriented to computational physics, theoretical chemistry and materials science.

Processed-data reproducibility package for ST-eUS/WHAM/Hummer/ISD analysis of CNFD passive permeation across a model lipid bilayer.

Automated GROMACS workflows for bile-salt systems: CG-to-atomistic backmapping, umbrella sampling and logP convergence analysis

tools for molecular dynamics: docking, metadynamics, umbrella sampling, high-throughput screening, etc.

Free-energy profile of lapachol crossing a POPC bilayer (GROMACS, CHARMM36, umbrella sampling). Work in progress, documented as an open notebook.

Reproducible GROMACS workflow for umbrella sampling, PMF calculation, and free-energy analysis.

Code and data for "Do neural-network free-energy surfaces know when they are wrong?" Tests the error bars of NN ensembles and a gradient GP, trained on umbrella-integration mean forces, against exact free energies (2D/4D models) and metadynamics for alanine dipeptide.

Monte Carlo package for simulating atoms interacting with non-bonded potentials

Plan, check and repair umbrella-sampling simulations: WHAM with bootstrap errors, diagnostics, repair windows and Gaussian-process umbrella integration with active learning.

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.