Tutorial on running Molecular Dynamics for GIST grid generation

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Tutorial written by Trent Balius (Jan. 9, 2017).


This is foremost for training in house Shoichet lab members. But we hope that the community finds this useful.

To use this tutorial you will need the following:

  • AMBER12 or higher.
  • GPUs to run AMBER on. In our case we uses an SGE queuing system to manage these jobs.
  • It is helpful if you have DOCK3.7 the latest version.


Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodynamic properties of water on GIST lattice.

Here, we will use these grids for DOCKing (although, there are many other uses).


  • download pdb
  • download pdb 4NVA form the PDB brake

Run GIST post processing

Combining GIST grids

Run convergence analysis