Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.
☆18Jun 21, 2022Updated 3 years ago
Alternatives and similar repositories for diffusion_analysis_MD_simulations
Users that are interested in diffusion_analysis_MD_simulations are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Analysis of Molecular Dynamics output in the IPython Notebook☆10Jan 24, 2017Updated 9 years ago
- C++ implementation of the Diffusion Map, with Python bindings☆10Aug 22, 2017Updated 8 years ago
- Software for automated processing of alchemical free energy calculations☆11Nov 7, 2022Updated 3 years ago
- This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.☆28Oct 1, 2020Updated 5 years ago
- ☆11Jan 5, 2022Updated 4 years ago
- PyEMMA Jupyter Notebooks☆14Jan 28, 2021Updated 5 years ago
- Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations☆20Mar 13, 2018Updated 8 years ago
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 11 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 3 months ago
- Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.☆12Feb 18, 2022Updated 4 years ago
- Implementation of corrections for diffusion coefficients in membrane simulations.☆10Aug 2, 2022Updated 3 years ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13Apr 11, 2025Updated 11 months ago
- Python script that creates 2D protein-ligand interaction images☆14Apr 23, 2018Updated 7 years ago
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆22Sep 26, 2024Updated last year
- A voxel based approach for dynamic cluster analysis of molecular dynamics trajectories.☆32Nov 5, 2025Updated 4 months ago
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- Plane-Wave density-functional theory (DFT) development for NWChemEx electronic structure software☆14Mar 18, 2026Updated last week
- Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.☆16Aug 12, 2022Updated 3 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39May 28, 2015Updated 10 years ago
- Gromacs topology template generator☆15Jul 15, 2021Updated 4 years ago
- This reaxFF LAMMPS script can be used to simulate the oxidation of nanomaterials, followed by cooling and thermal equilibration. Finally,…☆14Jul 29, 2022Updated 3 years ago
- ☆16Jul 28, 2022Updated 3 years ago
- post-processing package that performs analysis of structural, transport, and thermodynamic properties from ab initio molecular dynamics s…☆12Jan 9, 2026Updated 2 months ago
- Public repository for symmetry-adapted Gaussian Process Regression (SA-GPR)☆23Feb 3, 2025Updated last year
- Following Steve Brunton's book and code☆14Oct 23, 2022Updated 3 years ago
- Software package for FEP☆22Mar 3, 2026Updated 3 weeks ago
- Repository for material from the 2020 MC/MD Summer Workshop☆14Jul 12, 2024Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Nov 27, 2022Updated 3 years ago
- Zeobuilder is an extensible GUI-toolkit for molecular model construction.☆13Feb 15, 2019Updated 7 years ago
- persistent, pythonic trees for heterogeneous data☆33May 20, 2022Updated 3 years ago
- Main code repository for FATSLiM☆23Feb 13, 2022Updated 4 years ago
- numerical solution to 1D reaction diffusion equations☆12Sep 12, 2018Updated 7 years ago
- MDAnalysis home page mdanalysis.org as GitHub pages.☆14Feb 28, 2026Updated 3 weeks ago
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆24Jul 21, 2024Updated last year
- Notebooks for NYU Statistical Mechanics☆20Jul 6, 2023Updated 2 years ago
- Open Source Antibiotics Series 2☆10Jan 23, 2023Updated 3 years ago
- ☆10Mar 29, 2023Updated 2 years ago
- Protein preparation for MD, made faster and easier !☆15Dec 18, 2023Updated 2 years ago