Gromacs Preprocessed Topology (top) Parser

New in version 0.5.0.

Gromacs can produce preprocessed topology files that contain all topology information (generated using grompp -pp processed.top). Reading the regular topol.top is not supported, for now, since the #include statements are not handled. The TOP parser can read an write processed.top files. The TOP also provides an interface to modify the force-field terms and parameters in a programmatic way. Example applications involve system preparation for Hamiltonian-replica exchange (REST2 with lambda scaling), and automated force-field parametrization.

• Gromacs TOP file format
• Gromacs TOP - BLOCKS boiler-plate code