Project ID: plumID:19.028
Name: pRAVE
Archive: https://github.com/yhwang17/pRAVE/archive/master.zip
Category: methods
Keywords: RAVE, reaction coordinate, deep learning, metadynamics, kinetics
PLUMED version: 2.3
Contributor: Pratyush Tiwary
Submitted on: 04 May 2019
Publication: Y. Wang, J. M. Lamim Ribeiro, P. Tiwary, Past–future information bottleneck framework for simultaneously sampling biomolecular reaction coordinate, thermodynamics and kinetics, (2018)

PLUMED input files

File Compatible with
Lysozyme/round1/plumed.1.dat tested on v2.5 tested on master
Lysozyme/round10/plumed.10.2rc.dat tested on v2.5 tested on master
Lysozyme/round11/plumed.11.2rc.dat tested on v2.5 tested on master
Lysozyme/round13/plumed.13.2rc.1.dat tested on v2.5 tested on master
Lysozyme/round2/plumed.2.dat tested on v2.5 tested on master
Lysozyme/round3/plumed.3.dat tested on v2.5 tested on master
Lysozyme/round4/plumed.4.dat tested on v2.5 tested on master
Lysozyme/round5/plumed.5.dat tested on v2.5 tested on master
Lysozyme/round6/plumed.6.dat tested on v2.5 tested on master
Lysozyme/round7/plumed.7.dat tested on v2.5 tested on master
Lysozyme/round8/plumed.8.dat tested on v2.5 tested on master
Lysozyme/round9/plumed.9.2rc.dat tested on v2.5 tested on master
ala/round1/plumed.1.dat tested on v2.5 tested on master
ala/round2/plumed.2.dat tested on v2.5 tested on master
ala/round3/plumed.3.dat tested on v2.5 tested on master
ala/round4/plumed.4.dat tested on v2.5 tested on master
ala/unbiased/plumed.dat tested on v2.5 tested on master

Last tested: 18 Aug 2019, 14:17:01

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.

Submission history
[v1] 04 May 2019: original submission

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