Project ID: plumID:21.033
Name: Multiple-path-metadynamics applied to DNA base-pairing transitions
Archive: https://github.com/apdealbao/multipmd-dna/archive/refs/heads/main.zip
Category: bio
Keywords: path-CV, metadynamics, multiple-walker, dna
PLUMED version: 2.6
Contributor: Alberto Pérez-de-Alba-Ortíz
Submitted on: 04 Aug 2021
Last revised: 05 Aug 2021
Publication: A. Pérez de Alba Ortíz, J. Vreede, B. Ensing, Sequence dependence of transient Hoogsteen base pairing in DNA. PLOS Computational Biology. 18, e1010113 (2022)
PLUMED input files
Last tested: 22 Apr 2025, 10:14:11
Project description and instructions
This allows to run multiple-path-metadynamics on the Watson-Crick-Franklin to Hoogsteen base-pairing transition of an A-T pair in DNA. It requires PLUMED compiled with MPI and with the Path-CV code provided within. It also requires an MD engine that can run parallel replicas. We use GROMACS 2018.8 compiled with MPI.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 04 Aug 2021: original submission
[v2] 05 Aug 2021: updated doi
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