/ssRNA-MD

Molecular Dynamics simulation of single-stranded RNA molecules

Primary LanguageJupyter Notebook

ssRNA-MD

ML

Directory containing the source code for training neural networks to learn the distance array for atoms in MD simulation of RNA molecules in solutions with varying ions type and concentration

  • Variational Autoencoder (latent space regularized, t-SNE plots of encoded data from different MD runs cluster by concentrations of ions and types of ions)
  • Conditional Variational Autoencoder (work in progress)
    • Goal: generate prediction of distance array for out-of-distribution ions concentration

MD_sim

Directory containing the source code for running molecular dynamics simulation in varying ions concentration and types.

ARCHIVE

Code archive