Project ID: plumID:19.009
Name: RNA tetraloops folding
Archive: (browse)
Checksum (md5): 752da87e6f72a8f2cfe5aded0ed42bfd
Category: bio
Keywords: metadynamics, RNA, folding
PLUMED version: 2.4
Contributor: Giovanni Bussi
Submitted on: 16 Apr 2019
Publication: S. Bottaro, P. Banáš, J. Šponer, G. Bussi, Free Energy Landscape of GAGA and UUCG RNA Tetraloops, The Journal of Physical Chemistry Letters 7, 4032–4038 (2016)

PLUMED input files

File Compatible with
GAGA/ccGAGAgg.plumed.dat tested on v2.8 tested on master
UUCG/ccUUCGgg.plumed.dat tested on v2.8 tested on master

Last tested: 30 Nov 2021, 16:01:41

Project description and instructions
The zip files contains the trajectories discussed in the paper as well as a couple of plumed input files that were used for analysis. In order to run the metadynamics simulations described in the paper one should fix the metadynamics parameters (height and pace). In addition, histograms were computed using a syntax that changed in PLUMED 2.4. To use them with a more recent PLUMED they should be updated.

Submission history
[v1] 16 Apr 2019: original submission

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