Tutorial: Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory

Molecular Dynamics (MD) Simulations for the Grid Inhomogeneous Solvation Theory (GIST) Tutorial

This repository contains molecular dynamics simulations to support the tutorial hosted at https://github.com/liedllab/gist-tutorial.

The tutorial uses biotin-streptavidin as a test system to show GIST's merits.
As such, three MD simulations were run: biotin, streptavidin and the complex made up of them together.
All simulations were run using the AMBER simulation engine and follow AMBER's file conventions.
The simulations were run for a final duration of 100ns with 10 000 frames written out.
An input file with the used settings is uploaded in 100ns-npt-restraint.in.

For each simulation, the following files are made available here:

1. a .nc file, containing the coordinates of the system in NetCDF format.
2. a .parm7 file, containing the topology necessary to interpret the coordinates in AMBER parm format.
3. a .rst file, containing the starting structure of the simulation, i.e. the structure after equilibration.
4. a .out file, containing the AMBER output of the simulation run.
5. a .dat file, containing the results (grid) of the GIST analysis.