Project ID: plumID:19.028
Archive: https://github.com/yhwang17/pRAVE/archive/master.zip (browse)
Keywords: RAVE, reaction coordinate, deep learning, metadynamics, kinetics
PLUMED version: 2.3
Contributor: Pratyush Tiwary
Submitted on: 04 May 2019
Last revised: 19 Aug 2019
Publication: Y. Wang, J. M. L. Ribeiro, P. Tiwary, Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics, Nature Communications 10 (2019)
PLUMED input files
Last tested: 02 Jul 2020, 15:31:31
Project description and instructions
This needs PLUMED, GROMACS, tensorflow and Keras. Multiple rounds of MD and deep learning are performed to obtained converged reaction coordinate and free energy. All files for alanine dipeptide and benzene-T4L99A lysozyme are provided. Other info can be found here and here.
[v1] 04 May 2019: original submission
[v2] 19 Aug 2019: updated doi
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