Project ID: plumID:20.033
Name: COVID-19 Spike protein opening transition mechanism
Archive: https://github.com/vendruscolo-lab/Spike-OpeningTransitionEnsemble/raw/main/SpikeInput.zip
Category: bio
Keywords: EMMI, CryoEM, COVID-19, Spike, Metainference
PLUMED version: 2.6
Contributor: Faidon Brotzakis
Submitted on: 25 Nov 2020
Last revised: 04 Aug 2021
Publication: Z. F. Brotzakis, T. Löhr, M. Vendruscolo, Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy, Chemical Science (2021)

PLUMED input files

File Compatible with
ANALYSIS/plumed_histogram.dat tested on v2.8 tested on master
PRODUCTION/plumed.dat tested on v2.8 tested on master

Last tested: 30 Nov 2021, 15:33:44

Project description and instructions
The deposited input files contain the following directories. 1) The “TOPO_MDP” directory containing the GROMACS topology and parameter files. 2) The “PRODUCTION” directory containing the plumed input file for EMMI and the associated companion files such as an index file, data GMM file (SARS_COV2.dat) and pdb files for the definition of the CVs. 3) The “ANALYSIS” directory containing the plumed histogram file to project the 2D FES using the equilibrated trajectory data COLVAR_final of the EMMI simulations. More information can be found here. GROMACS 2018.6 double precision patched with PLUMED 2.6.0-dev was used.

Submission history
[v1] 25 Nov 2020: original submission
[v2] 04 Aug 2021: updated doi

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plumeDnest:20.033