Project ID: plumID:19.063
Name: Protein-ligand binding through metadynamics with path CVs
Archive: https://github.com/mbernett/zip_for_nest/raw/master/b2-AR_path.zip
Category: bio
Keywords: metadynamics, path CVs, ligand binding
PLUMED version: 2.1
Contributor: Mattia Bernetti
Submitted on: 17 Aug 2019
Last revised: 29 Aug 2019
Publication: M. Bernetti, M. Masetti, M. Recanatini, R. E. Amaro, A. Cavalli, An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes, Journal of Chemical Theory and Computation 15, 5689–5702 (2019)

PLUMED input files

File Compatible with
plumed_path.dat tested on v2.6 tested on master

Last tested: 18 Nov 2019, 15:24:04

Project description and instructions
Input file to carry out a well-tempered metadynamics simulation of the alprenolol-b2AR binding process using path CVs. The zip includes a structure file gro.gro file to use as initial configuration to launch the simulations, the corresponding topology file top.top, the plumed input file plumed_path.dat necessary to perform metadynamics with path CVs, and the GROMACS (version 4.6.7) parameter file prod.mdp where the simulations parameters are specified. The frameset.pdb file is the guess path necessary to use the path CVs.

Submission history
[v1] 17 Aug 2019: original submission
[v2] 29 Aug 2019: updated doi

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plumeDnest:19.063