Project ID: plumID:22.023
Name: Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy
Archive: https://github.com/vendruscolo-lab/IAPP/raw/main/IAPPInput.zip
Category: bio
Keywords: CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble
PLUMED version: 2.6-mod
Contributor: Faidon Brotzakis
Submitted on: 04 May 2022
Publication: Z. F. Brotzakis, T. Löhr, S. Truong, S. E. Hoff, M. Bonomi, M. Vendruscolo, Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy (2022)

PLUMED input files

File Compatible with
ANALYSIS/plumed_analysis.dat tested on v2.8 tested on master with custom code
ANALYSIS/plumed_analysis_unbiased.dat tested on v2.8 tested on master with custom code
PRODUCTION/plumed.dat tested on v2.8 tested on master with custom code

Last tested: 19 Nov 2022, 10:48:31

Project description and instructions
The TOPO_MDP folder containts GROMACS topology and parameter files. PRODUCTION contains the PLUMED file and the associated companion files such as an index file, data GMM file (iapp.dat), structure.pdb file and job submission file used. ANALYSIS folder contains the plumed_analysis.dat file used to print the CVs of the biased N-tail side as well as the final torrie-value weight per-frame. plumed_analysis_unbiased.dat is used to print the unbiased N-tail side CVs. The MEMMI method is implemented in the emmi-bias-sigmasem branch of the plumed master branch accessible here. More information can be found in here.

Submission history
[v1] 04 May 2022: original submission

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plumeDnest:22.023