Project ID: plumID:19.008
Name: anncolvar
Archive: https://archive.materialscloud.org/file/2019.0014/v1/anncolvar.zip
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 et al., 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 v2.6 tested on master
trpcage/mtd/plumed.dat tested on v2.6 tested on master
trpcage/ptmd/plumed.dat tested on v2.6 tested on master
trpcage/ptmtd/plumed.dat tested on v2.6 tested on master

Last tested: 13 Dec 2019, 20:35:19

Project description and instructions
Neural networks were created by ancolvar (https://github.com/spiwokv/anncolvar) 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 materialscloud.org

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plumeDnest:19.008