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, (2021)

PLUMED input files

File Compatible with
inside_path/plumed.0.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.1.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.10.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.11.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.2.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.3.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.4.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.5.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.6.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.7.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.8.dat tested on v2.8 tested on master with LOAD
inside_path/plumed.9.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.0.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.1.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.10.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.11.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.2.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.3.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.4.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.5.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.6.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.7.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.8.dat tested on v2.8 tested on master with LOAD
outside_path/plumed.9.dat tested on v2.8 tested on master with LOAD

Last tested: 30 Nov 2021, 15:14:31

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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plumeDnest:21.033