Project ID: plumID:19.008
Name: anncolvar
Category: methods
Keywords: neural network, dimensionality reduction
PLUMED version: 2.5.0
Contributor: Vojtech Spiwok
Submitted on: 16 Apr 2019
Last revised: 24 Apr 2019
Publication: D. Trapl, I. Horvacanin, V. Mareska, F. Ozcelik, G. Unal, V. Spiwok, Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations. Frontiers in Molecular Biosciences. 6 (2019)

PLUMED input files

File Compatible with
c8/plumed.dat tested on v2.9 tested on master
trpcage/mtd/plumed.dat tested on v2.9 tested on master
trpcage/ptmd/plumed.dat tested on v2.9 tested on master
trpcage/ptmtd/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 07:10:20

Project description and instructions
Neural networks were created by ancolvar ( and used to approximate Isomap CVs for 5 ns metadynamics of cyclooctane derivative and to approximate molecular surface area for 0.5 ns metadynamics, 1 ns parallel tempering and 1 ns parallel tempering metadynamics of Trp-cage folding with molecular surface area and alpha-RMSD CVs.

Submission history
[v1] 16 Apr 2019: original submission
[v2] 18 Apr 2019: updated DOI
[v3] 24 Apr 2019: zip moved to

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