Project ID: plumID:20.002
Name: Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study
Archive: https://github.com/rocello/P-NESTs_files/raw/master/GABAB1_zip-4-NEST.zip
Category: bio
Keywords: Metadynamics, path CVs
PLUMED version: 2.4
Contributor: Riccardo Ocello
Submitted on: 12 Feb 2020
Last revised: 23 May 2020
Publication: L. S. M. Evenseth, R. Ocello, M. Gabrielsen, M. Masetti, M. Recanatini, I. Sylte, A. Cavalli, Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. Journal of Chemical Information and Modeling. 60, 2294–2303 (2020)
PLUMED input files
| File | Compatible with |
|---|---|
| plumed-MetaD.dat |   |
Last tested: 20 Feb 2025, 20:51:04
Project description and instructions
The following plumed.dat script allows users to perform a Well-Tempered Metadynamics on Venus fly-trap GABAB receptor, in order to simulate conformational changes (open-to-closed), along the pathMSD CV previously parametrized from multiple classical MDs trajecories. All simulations were performed using GROMACS2016 and PLUMED 2.4
Submission history
[v1] 12 Feb 2020: original submission
[v2] 23 May 2020: updated doi
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