Project ID: plumID:19.001
Name: RNA SHAPE
Archive: https://github.com/srnas/shape-md/archive/4506611412ba0c88903483e814baec43b944453a.zip (browse)
Checksum (md5): d9bffa6c195093a4d30e88286d292e4f
Category: bio
Keywords: metadynamics, RNA, ligand binding
PLUMED version: 2.4
Contributor: Giovanni Bussi
Submitted on: 10 Apr 2019
Last revised: 03 Apr 2022
Publication: V. Mlýnský, G. Bussi, Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility. The Journal of Physical Chemistry Letters. 9, 313–318 (2018)
PLUMED input files
| File | Compatible with |
|---|---|
| plumed-g3.dat |   |
Last tested: 17 Jul 2025, 15:26:36
Project description and instructions
The zip file contains GROMACS topologies and input files together with a plumed example file. Notice that the simulations in the paper were performed using bias exchange metadynamics, and the example input correspond to a single replica (the one where ligand binding to residue 3 was enhanced). Input files for all replicas should be similarly created in order to run a real simulation.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 10 Apr 2019: original submission
[v2] 03 Apr 2022: fixed input for plumed nest (removed RESTART)
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