Project ID: plumID:19.020
Name: PTMetaD-WTE simulation of the Ntail IDP
Archive: https://github.com/mbernett/zip_for_nest/raw/master/Ntail.zip
Category: bio
Keywords: metadynamics, IDPs, protein folding
PLUMED version: 2.2
Contributor: Mattia Bernetti
Submitted on: 26 Apr 2019
Publication: M. Bernetti, M. Masetti, F. Pietrucci, M. Blackledge, M. R. Jensen, M. Recanatini, L. Mollica, A. Cavalli, Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations. The Journal of Physical Chemistry B. 121, 9572–9582 (2017)

PLUMED input files

File Compatible with
step-1/plumed.0.dat tested on v2.8 tested on master
step-1/plumed.1.dat tested on v2.8 tested on master
step-1/plumed.2.dat tested on v2.8 tested on master
step-1/plumed.3.dat tested on v2.8 tested on master
step-1/plumed.4.dat tested on v2.8 tested on master
step-1/plumed.5.dat tested on v2.8 tested on master
step-1/plumed.6.dat tested on v2.8 tested on master
step-1/plumed.7.dat tested on v2.8 tested on master
step-2/plumed.0.dat tested on v2.8 tested on master
step-2/plumed.1.dat tested on v2.8 tested on master
step-2/plumed.2.dat tested on v2.8 tested on master
step-2/plumed.3.dat tested on v2.8 tested on master
step-2/plumed.4.dat tested on v2.8 tested on master
step-2/plumed.5.dat tested on v2.8 tested on master
step-2/plumed.6.dat tested on v2.8 tested on master
step-2/plumed.7.dat tested on v2.8 tested on master

Last tested: 22 Jun 2022, 18:05:38

Project description and instructions
Input files for the simulation of the Ntail IDP using the PTMetaD-WTE scheme. The zip comprises two directories: step-1 and step-2. The former contains the equilibrated .gro files at each of the 8 temperatures considered, plus the plumed..dat necessary to enlarge the fluctuations of the potential energy by sampling the well-tempered ensemble (WTE) along with the GROMACS (version 4.6.7) .mdp files needed to launch the simulation. The second directory includes the plumed..dat files to subsequently combine this PT-WTE scheme with a metadynamics simulation using the radius of gyration and the alpha helical content as CVs, resulting in the PTMetaD-WTE framework.

Submission history
[v1] 26 Apr 2019: original submission

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plumeDnest:19.020