Project ID: plumID:21.025
Name: Computational and biochemical analysis of type IV pilus dynamics and stability
Archive: https://zenodo.org/record/4903970/files/T4P_MD_PLUMED.zip
Category: bio
Keywords: molecular dynamics, calcium binding, Type IV pilus
PLUMED version: 2.6
Contributor: Yasaman Karami
Submitted on: 07 Jun 2021
Last revised: 15 Dec 2021
Publication: Y. Karami, A. López-Castilla, A. Ori, J.-L. Thomassin, B. Bardiaux, T. Malliavin, N. Izadi-Pruneyre, O. Francetic, M. Nilges, Computational and biochemical analysis of type IV pilus dynamics and stability. Structure. 29, 1397-1409.e6 (2021)
PLUMED input files
Last tested: 22 Apr 2024, 20:49:46
Project description and instructions
All the input files (topology, setup, plumed files) for the MD simulations of the wild-type EHEC Type 4 Pilus studied in different conditions, i.e., in presence and absence of different ions, protonation states, and salt concentrations, as well as point mutations, are deposited here. The simulations were carried out using GROMACS 2019.4 package and PLUMED 2.6.0.
Submission history
[v1] 07 Jun 2021: original submission
[v2] 15 Dec 2021: updated doi
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