andrrizzi / tfep-revisited-2021View external linksLinks
Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials".
☆13Sep 14, 2021Updated 4 years ago
Alternatives and similar repositories for tfep-revisited-2021
Users that are interested in tfep-revisited-2021 are comparing it to the libraries listed below
Sorting:
- A library to perform targeted free energy perturbation with normalizing flows.☆10Sep 1, 2025Updated 5 months ago
- ☆31Jan 26, 2026Updated 3 weeks ago
- ☆44Feb 15, 2022Updated 4 years ago
- Software package for FEP☆22Feb 2, 2026Updated 2 weeks ago
- A Flow-based Variational Autoencoder for Molecule Generation☆10Feb 21, 2022Updated 3 years ago
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Feb 8, 2026Updated last week
- ☆25Oct 30, 2020Updated 5 years ago
- ☆12Dec 13, 2023Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46May 3, 2021Updated 4 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆31Feb 10, 2026Updated last week
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- TorchMD-NET. This is a simple code to train Schnet using pytorch-lighthing.☆11Nov 10, 2021Updated 4 years ago
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆16Dec 16, 2025Updated 2 months ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆17Feb 27, 2018Updated 7 years ago
- ☆93Dec 6, 2021Updated 4 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Jul 6, 2023Updated 2 years ago
- Collection of interaction and molecule parameters for the Martini3 force-field☆20Feb 7, 2023Updated 3 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Oct 24, 2025Updated 3 months ago
- A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.☆18Sep 12, 2023Updated 2 years ago
- Repository for MD methods and analysis from submitted or published work☆20Jun 10, 2023Updated 2 years ago
- ☆45Jan 16, 2026Updated last month
- ☆16Dec 24, 2016Updated 9 years ago
- High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)☆16May 3, 2023Updated 2 years ago
- Benchmark set for relative free energy calculations.☆119May 22, 2024Updated last year
- Implementation of methods to sample from Boltzmann distributions☆20Jan 24, 2023Updated 3 years ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆19Oct 31, 2025Updated 3 months ago
- Repository for Chemical Perception Sampling Tools☆21Aug 13, 2024Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆21Jun 6, 2024Updated last year
- The GB99dms implicit solvent force field for proteins, plus scripts and data☆27Sep 19, 2025Updated 4 months ago
- ☆53Oct 27, 2022Updated 3 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Dec 4, 2024Updated last year
- DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces☆20May 7, 2025Updated 9 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Nov 27, 2022Updated 3 years ago
- Infrastructure to implement and train NNPs☆23Updated this week
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆135May 24, 2024Updated last year
- some scripts for analysis of MD and CADD. And some tutorials.☆61Aug 12, 2024Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆22May 14, 2025Updated 9 months ago
- JAX exponential map normalising flows on sphere☆17Oct 4, 2020Updated 5 years ago