Project ID: plumID:23.033
Name: DNA G-quadruplex and G-hairpin folding with ST-metaD protocol
Archive: https://github.com/sponerlab/G4_folding_parallel/raw/main/archive.zip
Category: bio
Keywords: DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD
PLUMED version: 2.5.6
Contributor: Pavlína Pokorná
Submitted on: 16 Aug 2023
Publication: P. Pokorná, V. Mlýnský, G. Bussi, J. Šponer, P. Stadlbauer, Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble. International Journal of Biological Macromolecules. 261, 129712 (2024)

PLUMED input files

File Compatible with
plumed_inputs/G4_full_gHBfix_plumed.dat tested on v2.9 tested on master with LOAD
plumed_inputs/G4_full_plumed.dat tested on v2.9 tested on master
plumed_inputs/parallel_hairpin_HBfix_plumed.dat tested on v2.9 tested on master
plumed_inputs/parallel_hairpin_gHBfix_plumed.dat tested on v2.9 tested on master with LOAD
…nputs/parallel_hairpin_intertract_eRMSD_plumed.dat tested on v2.9 tested on master
plumed_inputs/parallel_hairpin_plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:46:58

Project description and instructions
Simulation setting and analysis files. PLUMED v. 2.5.6 and 2.7.3 were used with Gromacs v. 2018 and 2021, respectively. The gHBFIX PLUMED files deposited here are compatible with PLUMED v. 2.9 and newer versions.

Submission history
[v1] 16 Aug 2023: original submission

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plumeDnest:23.033