Project ID: plumID:20.032
Name: Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil
Keywords: clustering, conformational isomers
PLUMED version: 2.4
Contributor: Matteo Salvalaglio
Submitted on: 17 Nov 2020
Publication: V. Marinova, L. Dodd, S.-J. Lee, G. P. F. Wood, I. Marziano, M. Salvalaglio, Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering. Journal of Chemical Information and Modeling. 61, 2263–2273 (2021)
PLUMED input files
Last tested: 22 Jun 2022, 17:45:56
Project description and instructions
Examples of plumed files used to compute and print to file the instantaneous value of the 6 dihedral dihedral angles defining the conformational state of sildenafil in vacuum, solution and in the crystal phase. In solution the slowest of the dihedral angles is biased. The angles are used to construct 1D FES and to perform unsupervised clustering to identify highly populated conformational states.
[v1] 17 Nov 2020: original submission
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