Project ID: plumID:19.017
Name: Ligand binding pathways exploration
Category: bio
Keywords: metadynamics, ligand binding
PLUMED version: 2.5
Contributor: Riccardo Capelli
Submitted on: 23 Apr 2019
Last revised: 17 Jun 2019
Publication: R. Capelli, P. Carloni, M. Parrinello, Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics. The Journal of Physical Chemistry Letters. 10, 3495–3499 (2019)

PLUMED input files

File Compatible with
plumed_metad/metad_20ang.dat tested on v2.9 tested on master
plumed_metad/metad_22ang.dat tested on v2.9 tested on master
plumed_metad/metad_24ang.dat tested on v2.9 tested on master
plumed_metad/metad_26ang.dat tested on v2.9 tested on master
plumed_metad/metad_28ang.dat tested on v2.9 tested on master
plumed_reweight/reweight_rho_c.dat tested on v2.9 tested on master

Last tested: 18 Jun 2024, 14:38:39

Project description and instructions
The data are in three different folders: * input, which contains the GROMACS (2016.5) input files (gro, top, itp, and mdp) to run the MD simulation. * plumed_metad, which contains the PLUMED input file to perform volume-based metadynamics with different restraining potential size * plumed_reweight, which contains the PLUMED reweighing input file.

Submission history
[v1] 23 Apr 2019: original submission
[v2] 24 Apr 2019: corrected paths for input files (ndx, pdb, dat), example data files added for the reweighting procedure
[v3] 17 Jun 2019: doi added

For the Nature Methods paper by the PLUMED consortium (Nat. Methods 16, 670–673, 2019), Paolo Carloni acknowledges funding by the Deutsche Forschungsgemeinschaft- FOR 2518 DynIon project P6, and, along with Riccardo Capelli, the Human Brain Project.

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