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 et al., 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 v2.5 tested on master
step-1/plumed.1.dat tested on v2.5 tested on master
step-1/plumed.2.dat tested on v2.5 tested on master
step-1/plumed.3.dat tested on v2.5 tested on master
step-1/plumed.4.dat tested on v2.5 tested on master
step-1/plumed.5.dat tested on v2.5 tested on master
step-1/plumed.6.dat tested on v2.5 tested on master
step-1/plumed.7.dat tested on v2.5 tested on master
step-2/plumed.0.dat tested on v2.5 tested on master
step-2/plumed.1.dat tested on v2.5 tested on master
step-2/plumed.2.dat tested on v2.5 tested on master
step-2/plumed.3.dat tested on v2.5 tested on master
step-2/plumed.4.dat tested on v2.5 tested on master
step-2/plumed.5.dat tested on v2.5 tested on master
step-2/plumed.6.dat tested on v2.5 tested on master
step-2/plumed.7.dat tested on v2.5 tested on master

Last tested: 18 Aug 2019, 14:17:30

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