Project ID: plumID:19.032
Name: Chemical reaction in solution using path collective variables based on coordination patterns
Archive: https://github.com/physix-repo/plumed_input_pathcoordtable/raw/main/example-plumed2-pathcoordtable.zip
Category: chemistry
Keywords: chemical reactions, solutions, metadynamics, coordination patterns
PLUMED version: 2.4
Contributor: Fabio Pietrucci
Submitted on: 06 May 2019
Publication: F. Pietrucci, A. M. Saitta, Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios. Proceedings of the National Academy of Sciences. 112, 15030–15035 (2015)
PLUMED input files
| File | Compatible with |
|---|---|
| plumed.dat |   |
Last tested: 22 Apr 2024, 20:58:18
Project description and instructions
The input file plumed.dat defines a path collective variable based on distances between coordination patterns (tables of coordination numbers). In file path.pdb only two reference patterns, for the reactant and product state, are required, but more can be used if further information on the pathway is available. In this specific case the reaction goes from formamide to CO+NH3 in explicit water, and can be simulated, e.g., using quantum espresso or cp2k. A simple tool is also provided to simplify the creation of the path.pdb file.
Submission history
[v1] 06 May 2019: original submission
Badge
Click on the image below and get the code to add the badge to your website!
