Project ID: plumID:19.028
Name: pRAVE
Archive: https://github.com/yhwang17/pRAVE/archive/master.zip (browse)
Category: methods
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: ml><body><h1>503 Service Unavailable</h1> No server is available to handle this request. </body></html

PLUMED input files

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

Last tested: 15 Oct 2019, 20:06:04

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
[v2] 19 Aug 2019: updated doi

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plumeDnest:19.028