Project ID: plumID:23.040
Name: Supramolecular capsules assembly dynamics
Archive: https://github.com/riccardocapelli/papers_data/raw/master/capsule_assembly2023/input_data.zip
Category: chemistry
Keywords: Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics
PLUMED version: 2.6
Contributor: Riccardo Capelli
Submitted on: 06 Oct 2023
Publication: R. Capelli, G. Piccini, Atomistic Insights into Hydrogen-Bonded Supramolecular Capsule Self-Assembly Dynamics. The Journal of Physical Chemistry C. 128, 635–641 (2023)

PLUMED input files

File Compatible with
plumed_analysis/pyrogallolarene/plumed_rewCVs.dat tested on v2.9 tested on master
plumed_analysis/pyrogallolarene/plumed_solvent.dat tested on v2.9 tested on master
plumed_analysis/resorcinarene/plumed_rewCVs.dat tested on v2.9 tested on master
plumed_analysis/resorcinarene/plumed_solvent.dat tested on v2.9 tested on master
plumed_metad/plumed_pyro.dat tested on v2.9 tested on master
plumed_metad/plumed_reso.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:47:50

Project description and instructions
We performed for both resorcinarene and pyrogallolarene capsules a Well-Tempered metadynamics simulation, using GROMACS 2019.2 patched with PLUMED 2.6 (all the needed files for the GROMACS run are in the “input” folder, while the ones needed for plumed are in “plumed_metad” folder). The PLUMED input files for i) the calculation of the CVs used for the reweighting, ii) the calculation of the solvent molecules included in the capsules, and iii) the reweighting are in the “plumed_analysis” folder.

Submission history
[v1] 06 Oct 2023: original submission

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plumeDnest:23.040