Project ID: plumID:25.027
Name: Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information
Archive: https://github.com/mbernett/zip_for_nest/raw/master/saxs-xlms-md_rad.zip
Category: bio
Keywords: steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction
PLUMED version: 2.9
Contributor: Mattia Bernetti
Submitted on: 02 Sep 2025
Publication: V. Bresciani, F. Rinaldi, P. Franco, S. Girotto, A. Cavalli, J. D. Langer, M. Masetti, M. Bernetti, Integrating computational and experimental biophysics reveals novel insights into the RAD51-BRC4 interaction (2025)
PLUMED input files
Last tested: 11 Sep 2025, 17:56:37
Project description and instructions
Input files to carry out MD simulations of the RAD51-BRC4 complex using enhanced sampling methods, namely steered MD and metadynamics. The simulations integrate experimental information, specifically from SAXS in the steered MD and from XL-MS in the metad. The input folders contain all files required to perform the simulations, while the reweighting subfolder in the metad directory includes input files to compute metad weights a posteriori using the final bias. Simulations were conducted using GROMACS 2023.1 patched with PLUMED 2.9. All the files necessary to reproduce the analyses through a Jupyter Notebook are available on Zenodo under accession code 10.5281/zenodo.17035732.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 02 Sep 2025: original submission
Badge
Click on the image below and get the code to add the badge to your website!
