Project ID: plumID:19.032
Name: Chemical reaction in solution using path collective variables based on coordination patterns
Archive: https://sites.google.com/site/fabiopietrucci/Home/download/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 tested on v2.5 tested on master

Last tested: 18 Aug 2019, 14:16:52

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

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plumeDnest:19.032