insulin-dimer

This repository contains custom code for running and analyzing all-atom molecular dynamics (MD) simulations of insulin dimer dissociation, as described in ref. 1.

Note:
The code is shared to document the workflow implementation in ref. 1 and is not intended for direct execution.

Missing Components:

• Initial coordinates for running MD simulations
• Outputs such as MD trajectories, featurized trajectories, estimated committors, and TPT quantities, which are needed to link workflow steps.

Repository Structure

• mdrun: Files for running MD simulations.
  • scripts: Scripts for MD runs
  • inputs: Input topologies and force fields (initial coordinates are stored in [this][2])
• analysis: Files for DGA/TPT analysis of MD trajectories.

References

1. Jeong, et al. Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation