PLUMED-NEST

Project ID: plumID:19.074
Name: Asymmetric base pair opening in nucleic acids
Archive: https://github.com/bussilab/plumed-nest-colizzi-2019/archive/ae2f9a3ccedfc122cabc983a2d8f6ff02e2f5638.zip (browse)
Checksum (md5): 4426abdb18ef478ee210743389c33b14
Category: bio
Keywords: double helix, DNA, RNA, unwindability
PLUMED version: 2.5
Contributor: Giovanni Bussi
Submitted on: 04 Oct 2019
Last revised: 20 Oct 2019
Publication: F. Colizzi, C. Perez-Gonzalez, R. Fritzen, Y. Levy, M. F. White, J. C. Penedo, G. Bussi, Asymmetric base-pair opening drives helicase unwinding dynamics. Proceedings of the National Academy of Sciences. 116, 22471–22477 (2019)

PLUMED input files

File	Compatible with
DNA-AATT/3A5T/plumed.dat
DNA-AATT/3T5A/plumed.dat
DNA-CAGT/3A5T/plumed.dat
DNA-CAGT/3G5C/plumed.dat
DNA-CCGG/3C5G/plumed.dat
DNA-CCGG/3G5C/plumed.dat
DNA-CGGC/plumed.dat
DNA-GACT/3A5T/plumed.dat
DNA-GACT/3C5G/plumed.dat
DNA-TAAT/plumed.dat
RNA-AAUU/3A5U/plumed.dat
RNA-AAUU/3U5A/plumed.dat
RNA-CAGU/3A5U/plumed.dat
RNA-CAGU/3G5C/plumed.dat
RNA-CCGG/3C5G/plumed.dat
RNA-CCGG/3G5C/plumed.dat
RNA-CGGC/plumed.dat
RNA-GACU/3A5U/plumed.dat
RNA-GACU/3C5G/plumed.dat
RNA-UAAU/plumed.dat

Last tested: 22 Apr 2024, 20:56:54

Project description and instructions
Input files for unzipping simulations. Original simulations were done using PLUMED 1.3. This egg contains input files translated to PLUMED 2 syntax. Original input files can be seen in comments. Paper is just accepted.

Submission history
[v1] 04 Oct 2019: original submission
[v2] 20 Oct 2019: updated doi

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