Project ID: plumID:23.025
Name: Probing ion binding to G-quadruplexes and related events
Archive: https://github.com/mdpoleto/gq_ion_binding/archive/refs/heads/main.zip
Category: chemistry
Keywords: metadynamics, repulsive potential, nucleic acids, G-quadruplexes
PLUMED version: 2.7
Contributor: Marcelo Poleto
Submitted on: 29 Jun 2023
Last revised: 30 Oct 2023
Publication: M. D. Polêto, J. A. Lemkul, Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. Journal of Chemical Information and Modeling. 63, 6851–6862 (2023)
PLUMED input files
| File | Compatible with |
|---|---|
| …inder_metadynamics/1k8p/telomere_metady_cyl_K1.dat |   |
| cylinder_metadynamics/3ibk/terra_metady_cyl_K1.dat | |
| repulsive/1k8p/telomere_repulsive.dat | |
| repulsive/3ibk/terra_repulsive.dat | |
Last tested: 22 Apr 2025, 10:03:23
Project description and instructions
Plumed scripts used to run 1) volumed-based (cylinder) well tempered metadynamics simulations to probe ion binding to G-quadruplexes and 2) repulsive potential simulations (lower walls) to prevent ion binding. MD engine used is OpenMM v7.6.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 29 Jun 2023: original submission
[v2] 30 Oct 2023: updated doi
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