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1. MSRMD-CGMM MSRMD-CGMM Public

   This comprises the essential input files and scripts necessary for conducting constrained density functional theory (CDFT)-based fitting, as well as Multiscale Reactive Molecular Dynamics/Coarse-Gr…

   Python 2 2

2. Variational-Autoencoder Variational-Autoencoder Public

   Implementation of variational autoencoders (VAEs) for generating a large dataset of molecular structures along a reaction coordinate, given a small training dataset.

   Python

3. VAMPNet VAMPNet Public

   Code for VAMPNet analysis on AA trajectories

   Python

4. Equivariant-NNPs-for-bulk-water Equivariant-NNPs-for-bulk-water Public

   Final project - Structural and dynamical properties of liquid water using neural network potentials

   Python

5. NNP-CGMM NNP-CGMM Public

   This comprises the input codes and scripts required for running NNP/CG-MM simulations.

   Python

6. HIV-CG-RT HIV-CG-RT Public

   This comprises all codes and inputs for simulating HIV-1 capsid uncoating driven by reverse transcription.

   Shell