A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to perform replica exchanges
☆16Mar 4, 2024Updated 2 years ago
Alternatives and similar repositories for gromacs_plumed_hremd
Users that are interested in gromacs_plumed_hremd are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A tutorials suite for BioSimSpace.☆37Oct 22, 2025Updated 9 months ago
- Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.☆27Aug 15, 2024Updated last year
- Repository of the data for PLUMED Masterclass 22.3☆15Jul 10, 2024Updated 2 years ago
- Coarse-grained simulations of biomolecular complexes☆13Aug 2, 2023Updated 2 years ago
- For the purpose of post progressing of MD carried by gromacs☆24Jul 2, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆20Nov 10, 2021Updated 4 years ago
- ☆22Jul 14, 2023Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆45Jul 19, 2024Updated 2 years ago
- Graph-Based Force Fields Model to parameterize Force Fields by Graph Attention Networks☆10Apr 9, 2024Updated 2 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Jun 28, 2026Updated last month
- PaCS-Q is a Python toolkit designed to assist with Parallel Cascade Selection simulations (PaCS) for studying protein structural transiti…☆21Apr 30, 2026Updated 3 months ago
- ☆23Aug 25, 2023Updated 2 years ago
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆16May 7, 2026Updated 2 months ago
- SPMS table of pseudopotentials☆22Jan 22, 2023Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆18Jan 13, 2023Updated 3 years ago
- Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-co…☆22Jun 27, 2024Updated 2 years ago
- ☆15Jun 11, 2024Updated 2 years ago
- Using neural networks for enhanced sampling in computational biophysics☆16Aug 17, 2017Updated 8 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated 3 weeks ago
- development repository for PyInteraph2☆23Jun 18, 2026Updated last month
- ☆17Feb 3, 2026Updated 5 months ago
- Main code repository for the PLUMED-GUI plugin for VMD☆17Jan 22, 2026Updated 6 months ago
- ☆29May 5, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆26Oct 18, 2019Updated 6 years ago
- Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2☆44May 15, 2024Updated 2 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆323Updated this week
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆68Mar 29, 2026Updated 4 months ago
- Resources for and by the #codingForChemists Discord community!☆10Jun 18, 2023Updated 3 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆180Mar 11, 2026Updated 4 months ago
- A python package for performing GROMACS simulation ensembles☆22Jul 12, 2026Updated 2 weeks ago
- Matlab Simulation Package for Ab-initio Real-space Calculations☆32Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- ☆10Mar 6, 2025Updated last year
- Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information☆33Jul 16, 2026Updated last week
- NSU bioinformatics Python course☆13Sep 24, 2024Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Feb 11, 2021Updated 5 years ago
- OpenMM plugin to interface with PLUMED☆82Jan 15, 2026Updated 6 months ago
- Python based Graphical User Interface for generating input files for and running molecular dynamic simulation.☆10Aug 27, 2024Updated last year
- PyMOL plugin to calculate accessible contact volumes on PDB structures☆12Mar 17, 2025Updated last year