Project ID: plumID:19.065
Name: Molecular Enhanced Sampling with Autoencoders
Archive: https://github.com/weiHelloWorld/accelerated_sampling_with_autoencoder/raw/master/archive/plumed_adp.zip
Category: methods
Keywords: enhanced sampling, collective variables, deep learning
PLUMED version: 2.5
Contributor: Wei Chen
Submitted on: 06 Sep 2019
Publication: W. Chen, A. L. Ferguson, Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration, Journal of Computational Chemistry 39, 2079–2102 (2018)

PLUMED input files

File Compatible with
iter_10pc[-0.05,0.55].dat tested on v2.6 tested on master
iter_10pc[-0.15,-0.55].dat tested on v2.6 tested on master
iter_10pc[-0.15,0.55].dat tested on v2.6 tested on master
iter_10pc[-0.25,-0.55].dat tested on v2.6 tested on master
iter_10pc[-0.35,-0.55].dat tested on v2.6 tested on master
iter_10pc[-0.65,-0.45].dat tested on v2.6 tested on master
iter_10pc[-0.75,-0.35].dat tested on v2.6 tested on master
iter_10pc[-0.75,0.45].dat tested on v2.6 tested on master
iter_10pc[0.15,-0.65].dat tested on v2.6 tested on master
iter_10pc[0.25,-0.05].dat tested on v2.6 tested on master
iter_10pc[0.45,0.45].dat tested on v2.6 tested on master
iter_10pc[0.75,0.35].dat tested on v2.6 tested on master
iter_10pc[0.85,0.25].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.05].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.15].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.25].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.35].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.45].dat tested on v2.6 tested on master
iter_10pc[0.95,-0.65].dat tested on v2.6 tested on master
iter_10pc[0.95,0.05].dat tested on v2.6 tested on master
iter_1pc[-0.1,0.1].dat tested on v2.6 tested on master
iter_1pc[-0.1,0.3].dat tested on v2.6 tested on master
iter_1pc[-0.3,-0.1].dat tested on v2.6 tested on master
iter_1pc[-0.3,0.5].dat tested on v2.6 tested on master
iter_1pc[-0.5,-0.1].dat tested on v2.6 tested on master
iter_1pc[-0.5,0.7].dat tested on v2.6 tested on master
iter_1pc[-0.7,0.1].dat tested on v2.6 tested on master
iter_1pc[-0.7,0.3].dat tested on v2.6 tested on master
iter_1pc[-0.7,0.5].dat tested on v2.6 tested on master
iter_2pc[-0.1,-0.5].dat tested on v2.6 tested on master
iter_2pc[-0.1,-0.7].dat tested on v2.6 tested on master
iter_2pc[0.1,-0.3].dat tested on v2.6 tested on master
iter_2pc[0.1,-0.9].dat tested on v2.6 tested on master
iter_2pc[0.3,-0.3].dat tested on v2.6 tested on master
iter_2pc[0.3,-0.9].dat tested on v2.6 tested on master
iter_2pc[0.5,-0.5].dat tested on v2.6 tested on master
iter_2pc[0.7,-0.7].dat tested on v2.6 tested on master
iter_2pc[0.7,-0.9].dat tested on v2.6 tested on master
iter_3pc[-0.1,0.3].dat tested on v2.6 tested on master
iter_3pc[-0.1,0.7].dat tested on v2.6 tested on master
iter_3pc[-0.3,0.5].dat tested on v2.6 tested on master
iter_3pc[-0.5,0.5].dat tested on v2.6 tested on master
iter_3pc[-0.7,0.7].dat tested on v2.6 tested on master
iter_3pc[-0.9,0.9].dat tested on v2.6 tested on master
iter_3pc[0.1,0.3].dat tested on v2.6 tested on master
iter_3pc[0.3,0.5].dat tested on v2.6 tested on master
iter_3pc[0.3,0.7].dat tested on v2.6 tested on master
iter_3pc[0.3,0.9].dat tested on v2.6 tested on master
iter_4pc[-0.1,-0.1].dat tested on v2.6 tested on master
iter_4pc[-0.3,0.1].dat tested on v2.6 tested on master
iter_4pc[-0.5,0.3].dat tested on v2.6 tested on master
iter_4pc[-0.5,0.5].dat tested on v2.6 tested on master
iter_4pc[-0.5,0.7].dat tested on v2.6 tested on master
iter_4pc[-0.5,0.9].dat tested on v2.6 tested on master
iter_4pc[0.1,-0.1].dat tested on v2.6 tested on master
iter_4pc[0.1,0.5].dat tested on v2.6 tested on master
iter_4pc[0.3,-0.1].dat tested on v2.6 tested on master
iter_4pc[0.3,0.7].dat tested on v2.6 tested on master
iter_4pc[0.5,-0.1].dat tested on v2.6 tested on master
iter_4pc[0.7,0.1].dat tested on v2.6 tested on master
iter_4pc[0.7,0.3].dat tested on v2.6 tested on master
iter_4pc[0.9,0.5].dat tested on v2.6 tested on master
iter_5pc[-0.3,-0.9].dat tested on v2.6 tested on master
iter_5pc[-0.3,0.9].dat tested on v2.6 tested on master
iter_5pc[-0.5,-0.7].dat tested on v2.6 tested on master
iter_5pc[-0.5,0.9].dat tested on v2.6 tested on master
iter_5pc[-0.7,-0.1].dat tested on v2.6 tested on master
iter_5pc[-0.7,-0.3].dat tested on v2.6 tested on master
iter_5pc[-0.7,-0.5].dat tested on v2.6 tested on master
iter_5pc[-0.7,0.1].dat tested on v2.6 tested on master
iter_5pc[-0.7,0.3].dat tested on v2.6 tested on master
iter_5pc[-0.7,0.5].dat tested on v2.6 tested on master
iter_5pc[-0.7,0.7].dat tested on v2.6 tested on master
iter_5pc[0.3,0.9].dat tested on v2.6 tested on master
iter_5pc[0.5,-0.9].dat tested on v2.6 tested on master
iter_5pc[0.5,0.7].dat tested on v2.6 tested on master
iter_5pc[0.7,-0.9].dat tested on v2.6 tested on master
iter_5pc[0.7,0.5].dat tested on v2.6 tested on master
iter_5pc[0.9,-0.1].dat tested on v2.6 tested on master
iter_5pc[0.9,-0.7].dat tested on v2.6 tested on master
iter_5pc[0.9,0.1].dat tested on v2.6 tested on master
iter_5pc[0.9,0.3].dat tested on v2.6 tested on master
iter_6pc[-0.05,-0.95].dat tested on v2.6 tested on master
iter_6pc[-0.15,-0.95].dat tested on v2.6 tested on master
iter_6pc[-0.35,-0.85].dat tested on v2.6 tested on master
iter_6pc[-0.35,0.75].dat tested on v2.6 tested on master
iter_6pc[-0.45,0.65].dat tested on v2.6 tested on master
iter_6pc[-0.55,-0.75].dat tested on v2.6 tested on master
iter_6pc[-0.55,0.55].dat tested on v2.6 tested on master
iter_6pc[-0.65,-0.65].dat tested on v2.6 tested on master
iter_6pc[-0.65,0.15].dat tested on v2.6 tested on master
iter_6pc[0.05,-0.95].dat tested on v2.6 tested on master
iter_6pc[0.25,-0.85].dat tested on v2.6 tested on master
iter_6pc[0.35,0.45].dat tested on v2.6 tested on master
iter_6pc[0.45,-0.75].dat tested on v2.6 tested on master
iter_6pc[0.45,0.75].dat tested on v2.6 tested on master
iter_6pc[0.55,-0.65].dat tested on v2.6 tested on master
iter_6pc[0.55,0.75].dat tested on v2.6 tested on master
iter_6pc[0.65,-0.45].dat tested on v2.6 tested on master
iter_6pc[0.65,0.35].dat tested on v2.6 tested on master
iter_6pc[0.75,0.55].dat tested on v2.6 tested on master
iter_6pc[0.75,0.75].dat tested on v2.6 tested on master
iter_7pc[-0.05,-0.75].dat tested on v2.6 tested on master
iter_7pc[-0.05,0.15].dat tested on v2.6 tested on master
iter_7pc[-0.15,-0.35].dat tested on v2.6 tested on master
iter_7pc[-0.15,0.05].dat tested on v2.6 tested on master
iter_7pc[-0.25,-0.85].dat tested on v2.6 tested on master
iter_7pc[-0.35,-0.85].dat tested on v2.6 tested on master
iter_7pc[-0.35,0.05].dat tested on v2.6 tested on master
iter_7pc[-0.45,0.05].dat tested on v2.6 tested on master
iter_7pc[-0.55,-0.85].dat tested on v2.6 tested on master
iter_7pc[-0.65,-0.15].dat tested on v2.6 tested on master
iter_7pc[-0.65,-0.95].dat tested on v2.6 tested on master
iter_7pc[0.05,0.15].dat tested on v2.6 tested on master
iter_7pc[0.15,0.15].dat tested on v2.6 tested on master
iter_7pc[0.25,0.05].dat tested on v2.6 tested on master
iter_7pc[0.35,-0.05].dat tested on v2.6 tested on master
iter_7pc[0.45,-0.15].dat tested on v2.6 tested on master
iter_7pc[0.45,-0.65].dat tested on v2.6 tested on master
iter_7pc[0.55,-0.35].dat tested on v2.6 tested on master
iter_7pc[0.55,-0.45].dat tested on v2.6 tested on master
iter_7pc[0.55,-0.55].dat tested on v2.6 tested on master
iter_8pc[-0.05,-0.05].dat tested on v2.6 tested on master
iter_8pc[-0.05,-0.15].dat tested on v2.6 tested on master
iter_8pc[-0.05,0.75].dat tested on v2.6 tested on master
iter_8pc[-0.15,-0.85].dat tested on v2.6 tested on master
iter_8pc[-0.15,0.65].dat tested on v2.6 tested on master
iter_8pc[-0.25,-0.75].dat tested on v2.6 tested on master
iter_8pc[-0.25,0.55].dat tested on v2.6 tested on master
iter_8pc[-0.35,0.25].dat tested on v2.6 tested on master
iter_8pc[-0.45,-0.35].dat tested on v2.6 tested on master
iter_8pc[0.05,-0.15].dat tested on v2.6 tested on master
iter_8pc[0.15,-0.05].dat tested on v2.6 tested on master
iter_8pc[0.15,-0.85].dat tested on v2.6 tested on master
iter_8pc[0.25,-0.15].dat tested on v2.6 tested on master
iter_8pc[0.25,-0.95].dat tested on v2.6 tested on master
iter_8pc[0.35,-0.95].dat tested on v2.6 tested on master
iter_8pc[0.45,-0.95].dat tested on v2.6 tested on master
iter_8pc[0.55,-0.95].dat tested on v2.6 tested on master
iter_8pc[0.65,-0.85].dat tested on v2.6 tested on master
iter_8pc[0.75,-0.55].dat tested on v2.6 tested on master
iter_8pc[0.75,0.05].dat tested on v2.6 tested on master
iter_9pc[-0.65,-0.65].dat tested on v2.6 tested on master
iter_9pc[-0.75,0.15].dat tested on v2.6 tested on master
iter_9pc[-0.75,0.45].dat tested on v2.6 tested on master
iter_9pc[-0.85,-0.45].dat tested on v2.6 tested on master
iter_9pc[-0.95,-0.15].dat tested on v2.6 tested on master
iter_9pc[-0.95,-0.35].dat tested on v2.6 tested on master
iter_9pc[0.05,-0.05].dat tested on v2.6 tested on master
iter_9pc[0.05,-0.75].dat tested on v2.6 tested on master
iter_9pc[0.15,0.05].dat tested on v2.6 tested on master
iter_9pc[0.45,0.45].dat tested on v2.6 tested on master
iter_9pc[0.55,-0.05].dat tested on v2.6 tested on master
iter_9pc[0.65,-0.25].dat tested on v2.6 tested on master
iter_9pc[0.65,0.35].dat tested on v2.6 tested on master
iter_9pc[0.75,0.25].dat tested on v2.6 tested on master
iter_9pc[0.85,-0.65].dat tested on v2.6 tested on master
iter_9pc[0.85,0.05].dat tested on v2.6 tested on master
iter_9pc[0.95,-0.15].dat tested on v2.6 tested on master
iter_9pc[0.95,-0.25].dat tested on v2.6 tested on master
iter_9pc[0.95,-0.35].dat tested on v2.6 tested on master
iter_9pc[0.95,-0.45].dat tested on v2.6 tested on master

Last tested: 18 Nov 2019, 15:23:55

Project description and instructions
These files are used to run umbrella sampling on autoencoder CVs for analine dipeptide. They were generated from autoencoder training using simulation data (which were done outside PLUMED, using deep learning packages such as Keras), and can be used with any simulation engine and PLUMED with “annfunc” module installed. Naming convention: iter_n_pc_[x,y].dat is the file for umbrella sampling in iteration n with [x,y] as the potential center in autoencoder CV space. For more information, please check out here and here.

Submission history
[v1] 06 Sep 2019: original submission

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plumeDnest:19.065