CGMap provides a tool to map fine-grained (FG) molecular dynamics trajectories to coarse-grained (CG) trajectories. The map between FG and CG trajectories is constrained to be linear and time invariant, with weights defined as either corresponding to center of points, center of mass, or center of charge, although the user is able to modify this in a manual way (see test cases). The code is able to automatically detect and modify the contributing weight of atoms shared between CG sites in a single molecule if the appropriate options are enabled (see test cases).

This code is in beta. Please report bugs on the GitHub bug tracker. Regression tests are provided. Note that numerical differences in underlying libraries (through numpy) often create slightly different outputs.

Periodic boundary issues are handled: atoms are moved to the smallest local image before mapping, and moved back to the image where the most contributing atoms were present. Alternatively, options are available to atomatically wrap the CG representation after it is produced in the local minimal image.

See the test directory for many cases of example usage. No command line interface is present, nor planned.