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 2024, 20:51:57
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.
Submission history
[v1] 04 Aug 2021: original submission
[v2] 05 Aug 2021: updated doi
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