Project ID: plumID:20.007
Name: Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics
Archive: https://github.com/tiwarylab/T4-lysozyme-loop/raw/master/archive/nest.zip
Category: bio
Keywords: metadynamics, loop movement, artificial intelligence
PLUMED version: 2.4.2
Contributor: Pratyush Tiwary
Submitted on: 07 Apr 2020
Last revised: 05 Oct 2020
Publication: Z. Smith, P. Ravindra, Y. Wang, R. Cooley, P. Tiwary, Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics, The Journal of Physical Chemistry B 124, 8221–8229 (2020)

PLUMED input files

File Compatible with
double/plumed.dat tested on v2.6 tested on master
single/plumed.dat tested on v2.6 tested on master
triple/plumed.dat tested on v2.6 tested on master

Last tested: 18 Oct 2020, 14:53:05

Project description and instructions
Use md.tpr to run GROMACS (version 2016.5p2.4.2) patched with PLUMED 2.4.2 using plumed.dat. The rmsd.pdb files are used for the quadratic wall preventing the systems from exploring conformations with distorted secondary structure. No wall was used for the triple mutant.

Submission history
[v1] 07 Apr 2020: original submission
[v2] 23 May 2020: updated doi
[v3] 05 Oct 2020: updated doi

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plumeDnest:20.007