PLUMED-NEST

Project ID: plumID:24.020
Name: Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics
Archive: https://github.com/connorzzou/PLUMED-NEST/raw/main/PLUMED_GNN_SPIB.zip
Category: bio
Keywords: LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning
PLUMED version: 2.8.1
Contributor: Ziyue Zou, Dedi Wang, Pratyush Tiwary
Submitted on: 22 Sep 2024
Publication: Ziyue Zou, Dedi Wang, Pratyush Tiwary. Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

PLUMED input files

File	Compatible with
ala2/imetad/plumed_phi_10000.dat
ala2/imetad/plumed_phi_2000.dat
ala2/imetad/plumed_phi_50000.dat
ala2/imetad/plumed_psi_10000.dat
ala2/imetad/plumed_psi_2000.dat
ala2/imetad/plumed_psi_50000.dat
ala2/imetad/plumed_z1z2_10000.dat
ala2/imetad/plumed_z1z2_2000.dat
ala2/imetad/plumed_z1z2_50000.dat
ala2/wtmetad/plumed_ang.dat
ala2/wtmetad/plumed_gnn.dat
ala3/imetad/plumed_phi_1000.dat
ala3/imetad/plumed_phi_200.dat
ala3/imetad/plumed_phi_5000.dat
ala3/imetad/plumed_psi_1000.dat
ala3/imetad/plumed_psi_200.dat
ala3/imetad/plumed_psi_5000.dat
ala3/imetad/plumed_z1z2_1000.dat
ala3/imetad/plumed_z1z2_200.dat
ala3/imetad/plumed_z1z2_5000.dat

Last tested: 23 Apr 2025, 10:12:03

Project description and instructions
Software used was PLUMED-2.8.1 with PYTORCH module, GROMACS 2021.6 (alanine tetrapeptide), and GROMACS 2019.6 (alanine dipeptide)

Submission history
[v1] 22 Sep 2024: original submission

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