Input files for GROMACS tutorials written for the Journal of Physical Chemistry B
☆24Jul 21, 2024Updated last year
Alternatives and similar repositories for gmx_tutorials_jpcb
Users that are interested in gmx_tutorials_jpcb are comparing it to the libraries listed below
Sorting:
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆22Sep 26, 2024Updated last year
- ☆16Jul 28, 2022Updated 3 years ago
- CHAPERONg: An automated pipeline for GROMACS MD simulations and trajectory analyses☆60Aug 2, 2025Updated 7 months ago
- Some of useful tcl scripts to analyse data from VMD☆15Aug 2, 2022Updated 3 years ago
- ☆11Oct 23, 2025Updated 4 months ago
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆35Mar 12, 2026Updated last week
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Jan 26, 2022Updated 4 years ago
- Notebooks for NYU Statistical Mechanics☆20Jul 6, 2023Updated 2 years ago
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆42Jan 29, 2026Updated last month
- An interoperable Python framework for biomolecular simulation.☆147Updated this week
- Pipeline converting PDB files to docking-ready PDBQT format☆21Apr 23, 2025Updated 10 months ago
- Software for automated processing of alchemical free energy calculations☆11Nov 7, 2022Updated 3 years ago
- ☆45Jan 8, 2026Updated 2 months ago
- A conda-smithy repository for ambertools.☆11Updated this week
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆23Feb 2, 2024Updated 2 years ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆247Feb 18, 2026Updated last month
- scripts for analyzing molecular dynamics trajectories using VMD☆39May 28, 2015Updated 10 years ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆10Sep 17, 2025Updated 6 months ago
- ☆31Dec 4, 2022Updated 3 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Nov 25, 2025Updated 3 months ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Nov 11, 2021Updated 4 years ago
- Machine learning for molecular dynamics☆13Jan 9, 2025Updated last year
- Perform operations on chemical structures using Python.☆13Updated this week
- Calculation of water/solvent partition coefficients with Gromacs.☆29Oct 14, 2024Updated last year
- Use AutoDock for Ligand-based Virtual Screening☆22Aug 18, 2024Updated last year
- Density based object completion over PBC.☆30Dec 10, 2024Updated last year
- ☆70Jul 19, 2023Updated 2 years ago
- ☆13Jun 11, 2024Updated last year
- Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆15Mar 4, 2026Updated 2 weeks ago
- Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.☆12Feb 18, 2022Updated 4 years ago
- Xlink is a Python script that uses Gromacs to automatically perfom simulation crosslinking and generate atomistic model of aromatic polya…☆16Jul 8, 2023Updated 2 years ago
- A collection of PyMOL plugins to visualize atomic bonds.☆22Sep 2, 2020Updated 5 years ago
- Geometric super-resolution for molecular geometries☆42Jun 15, 2022Updated 3 years ago
- Best practice document for alchemical free energy calculations going to livecoms journal☆85Feb 25, 2026Updated 3 weeks ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13Apr 11, 2025Updated 11 months ago
- Generates Martini models for open carbon nanotubes to use with Gromacs.☆15Nov 24, 2021Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆45Feb 6, 2026Updated last month
- Fully automated docking pipeline (can be run in distributed environments)☆55Updated this week
- Weighted Ensemble Data Analysis and Plotting☆26Dec 11, 2025Updated 3 months ago