Examples

Mapping a pentane molecule

This example defines a topology file for a coarse-grained pentane molecule. The molecule is composed of 17 atoms and we mapped it to a coarse-grained representation of the molecule composed of 5 beads. Every carbon and its connected hydrogens is mapped to one coarse-grained bead.

The below link will open a project with a pentane molecule loaded. The input file and the resulting topology XML file are available here: pentane_cg.pdb, pentane.xml.

Mapping a polyalanine molecule

In this example, we mapped a polyalanine molecule with composed of 103 atoms to a 51-bead coarse-grained representation. We coarse-grain the molecule such that each heavy atom with its attached hydrogen(s) is mapped to one coarse-grained bead.

The below link will open a project with a polyalanine molecule loaded. The input file and the resulting topology XML file are available here: polyalanine_cg.pdb, polyalanine.xml.

If you use this tool, please cite:
S. Bevc, C. Junghans, M. Praprotnik (2015) STOCK: Structure mapper and online coarse-graining kit for molecular simulations. Journal of Computational Chemistry, 36, 467, doi: 10.1002/jcc.23806 (Link, BibteX)