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 tested on v2.9 tested on master
cylinder_metadynamics/3ibk/terra_metady_cyl_K1.dat tested on v2.9 tested on master
repulsive/1k8p/telomere_repulsive.dat tested on v2.9 tested on master
repulsive/3ibk/terra_repulsive.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:46:37

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.

Submission history
[v1] 29 Jun 2023: original submission
[v2] 30 Oct 2023: updated doi

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plumeDnest:23.025