Using supervised machine learning to build collective variables for accelerated sampling
☆28Jun 26, 2018Updated 7 years ago
Alternatives and similar repositories for SML_CV
Users that are interested in SML_CV are comparing it to the libraries listed below
Sorting:
- Fast PBC wrapping and unwrapping for VMD☆24Nov 25, 2024Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated last month
- ☆11Oct 18, 2019Updated 6 years ago
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆15Jun 23, 2020Updated 5 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 6 years ago
- Automatic Mutual Information Noise Omission☆16Oct 8, 2024Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Feb 19, 2026Updated last week
- Using neural networks for enhanced sampling in computational biophysics☆16Aug 17, 2017Updated 8 years ago
- Get access to our MD data files.☆31Nov 22, 2023Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 5 years ago
- VMD Plugin and associated scripts to build lignin structures from topological specifications☆17Jul 17, 2025Updated 7 months ago
- Package for reading, analysis and visualization of metadynamics HILLS☆39Nov 28, 2023Updated 2 years ago
- Scripts for PCA and related analyses of lipid motions☆10Jun 21, 2022Updated 3 years ago
- Main repository for METAGUI3☆20Jun 19, 2021Updated 4 years ago
- A library for converting molecular topologies☆13May 20, 2015Updated 10 years ago
- VMD plugin to calculate and visualize clusters of conformations for a trajectory☆23Oct 24, 2018Updated 7 years ago
- Development version of plumed 2☆483Updated this week
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Implementation of corrections for diffusion coefficients in membrane simulations.☆10Aug 2, 2022Updated 3 years ago
- Package for reading, analysis and visualization of metadynamics HILLS with 3 collective variables (addendum to metadynminer)☆11Apr 29, 2022Updated 3 years ago
- Tree Search Molecular Dynamics Simulation☆11Aug 25, 2019Updated 6 years ago
- Collective variables library for molecular simulation and analysis programs☆236Feb 17, 2026Updated last week
- Analyse Rotational Diffusion Tensor from MD Simulations☆22Oct 31, 2024Updated last year
- OpenMM testbed for constant-pH methodologies.☆24Sep 20, 2021Updated 4 years ago
- Convenience functions for VMD-TCL scripting☆14Jul 16, 2025Updated 7 months ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆14Sep 14, 2018Updated 7 years ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- ☆12Jan 1, 2019Updated 7 years ago
- How to analyze molecular dynamics data with PyEMMA☆84May 29, 2019Updated 6 years ago
- An open source Python framework for transition interface and path sampling calculations.☆116Updated this week
- 4D Genome Reconstruction and Dynamics Prediction: Maximum Entropy Based HI-C/Distance Map - Polymer Physics - Structures Method☆13Feb 16, 2026Updated last week
- Calculate position-dependent diffusivity functions from trajectory data (usually from molecular dynamics). The approach is described in h…☆11Mar 25, 2025Updated 11 months ago
- A Python package to improve the accessibility and reproducibility of enhanced sampling simulations☆15May 16, 2018Updated 7 years ago
- Learning Protein-Ligand Properties with Atomic Environment Vectors☆10Apr 19, 2024Updated last year
- Normal Mode Analysis for Macromolecules☆18Apr 1, 2017Updated 8 years ago
- 🚂 Python API for Emma's Markov Model Algorithms 🚂☆337Sep 11, 2023Updated 2 years ago
- A unified framework for machine learning collective variables for enhanced sampling simulations☆135Feb 19, 2026Updated last week