@@ -62,6 +62,10 @@ Example mapping and bond definition files are present in the ``test/data`` direc
After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created. The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided. The itp file contains the parameters for each molecule type.
It is important to perform validation of any new parameter set.
This is typically done by comparing properties between the reference simulation and simulations using the new CG model.
In the tutorial we use the radius of gyration, but there are many other suitable properties, depending on the class of molecule being parametrised.
Mapping / Bond Definition Files
-------------------------------
The mapping and bond definition input files use a format similar to the GROMACS itp/top format.