Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
☆21Mar 13, 2018Updated 8 years ago
Alternatives and similar repositories for PyDHAMed
Users that are interested in PyDHAMed are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- (outdated) fork of https://gitlab.com/gromacs/gromacs☆53Apr 27, 2023Updated 2 years ago
- BioEn - Bayesian Inference Of ENsembles☆23Feb 6, 2024Updated 2 years ago
- A domain specific language for creating scientific pipelines☆15Mar 29, 2026Updated last week
- Learning free energy landscapes using artificial neural networks☆14Nov 30, 2017Updated 8 years ago
- Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accomp…☆13Mar 28, 2018Updated 8 years ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆81Sep 5, 2024Updated last year
- a python package for the interfacial analysis of molecular simulations☆94Updated this week
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- ☆19Feb 6, 2017Updated 9 years ago
- Gibbs sampling for expanded ensembles and replica exchange simulations☆11Jun 1, 2014Updated 11 years ago
- GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).☆188Sep 4, 2025Updated 7 months ago
- Python Tools for NAMD☆24May 7, 2025Updated 11 months ago
- Analyse Rotational Diffusion Tensor from MD Simulations☆22Oct 31, 2024Updated last year
- A Python module for scripting with Q-Chem☆14Aug 16, 2022Updated 3 years ago
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- the simple alchemistry library☆235Jan 23, 2026Updated 2 months ago
- C++ Accelerated Python Diffusion Maps Library☆23Aug 28, 2018Updated 7 years ago
- Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.☆18Jun 21, 2022Updated 3 years ago
- ☆15Jun 26, 2018Updated 7 years ago
- Membrane protein builder and parameterizer☆19Sep 1, 2024Updated last year
- "Computational modeling and visualization" resource repository☆33Mar 11, 2023Updated 3 years ago
- GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the …☆11Apr 7, 2023Updated 3 years ago
- A python framework to run adaptive Markov state model (MSM) simulation on HPC resources☆17Aug 1, 2025Updated 8 months ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- NordVPN Threat Protection Pro™ • AdTake your cybersecurity to the next level. Block phishing, malware, trackers, and ads. Lightweight app that works with all browsers.
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆295Feb 12, 2026Updated last month
- Software Suite for Advanced General Ensemble Simulations☆90Feb 24, 2023Updated 3 years ago
- Force Fields☆14Oct 25, 2022Updated 3 years ago
- Implementation of corrections for diffusion coefficients in membrane simulations.☆10Aug 2, 2022Updated 3 years ago
- Analysis of non-covalent interactions in MD trajectories☆68Jan 3, 2025Updated last year
- GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collectiv…☆12Feb 20, 2024Updated 2 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆66Nov 26, 2025Updated 4 months ago
- A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.☆32Nov 5, 2025Updated 5 months ago
- 2D Ising model in C++, including IPython notebook examples☆11Nov 14, 2019Updated 6 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Prepare topology and coordinate file for CG models in Genesis.☆13Jul 3, 2025Updated 9 months ago
- 🚂 Python API for Emma's Markov Model Algorithms 🚂☆339Sep 11, 2023Updated 2 years ago
- Convert PDB files to LAMMPS data and force field files.☆20Oct 9, 2017Updated 8 years ago
- Ramachandran plotting tool☆21Mar 31, 2026Updated last week
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- Reads Gromacs EDR file to populate a pandas dataframe☆33Oct 12, 2025Updated 5 months ago
- Repository for material from the 2020 MC/MD Summer Workshop☆14Jul 12, 2024Updated last year