Project ID: plumID:19.001
Name: RNA SHAPE
Archive: https://github.com/srnas/shape-md/archive/476e47196772e5dc109018bc4c2447c5dc234381.zip (browse)
Checksum (md5): 12877107e2d86627750c4461eae5ac38
Keywords: metadynamics, RNA, ligand binding
PLUMED version: 2.4
Contributor: Giovanni Bussi
Submitted on: 10 Apr 2019
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
Last tested: 08 Apr 2020, 08:47:16
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.
[v1] 10 Apr 2019: original submission
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