Project ID: plumID:19.017
Name: Ligand binding pathways exploration
Archive: https://github.com/riccardocapelli/papers_data/raw/master/pathway_search2019/input_data.zip
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: 27 Mar 2024, 17:12:22

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

Acknowledgement
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.

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:19.017