Project ID: plumID:19.009
Name: RNA tetraloops folding
Archive: https://github.com/srnas/tetraloops-trajectories/archive/48a88a7fb3941cf8033120a61179bf5243bb74a8.zip (browse)
Checksum (md5): b30b145f2a6e4f1b32552bc93025e48a
Category: bio
Keywords: metadynamics, RNA, folding
PLUMED version: 2.4
Contributor: Giovanni Bussi
Submitted on: 16 Apr 2019
Last revised: 03 Apr 2022
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: 20 May 2022, 09:15:41

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
[v2] 03 Apr 2022: fixed input for plumed nest (removed RESTART)

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