Quick guide

These instructions will guide you through a simple example of coarse-graining water molecules. The coarse-grained model is set up by mapping a water molecule to a one-bead representation located at the center of mass of molecule. It will only cover the first three iterations.

When you enter, the browser window will be split in two frames. The upper frame has a regular STOCK web page, and the bottom frame has instructions that will guide you through the process. You can click and drag the border between the two frames to resize them and set it so that it fits your needs.

For the sake of this quick guide, we provide here the necessary distribution files. These files would otherwise be obtained by running MD simulations.

Plase save these distribution files somewhere on your computer (right-click and select "Save link as ..."):

  • rdf_cgcg_tgt (target water-water atomistic distribution)
  • rdf_cgcg_0 (iteration 0 water-water coarse-grained distribution)
  • rdf_cgcg_1 (iteration 1 water-water coarse-grained distribution)
  • rdf_cgcg_2 (iteration 2 water-water coarse-grained distribution)
  • rdf_cgcg_3 (iteration 3 water-water coarse-grained distribution)

To exit the quick guide, click on exit quick guide in the upper right corner of the instructions frame. You will also exit by going through all steps.