Topologies¶
GROMACS must know on which atoms and combinations of atoms the various contributions to the potential functions (see chapter Interaction function and force fields) must act. It must also know what parameters must be applied to the various functions. All this is described in the topology file top, which lists the constant attributes of each atom. There are many more atom types than elements, but only atom types present in biological systems are parameterized in the force field, plus some metals, ions and silicon. The bonded and special interactions are determined by fixed lists that are included in the topology file. Certain non-bonded interactions must be excluded (first and second neighbors), as these are already treated in bonded interactions. In addition, there are dynamic attributes of atoms - their positions, velocities and forces. These do not strictly belong to the molecular topology, and are stored in the coordinate file gro (positions and velocities), or trajectory file trr (positions, velocities, forces).
This chapter describes the setup of the topology file, the top file and the database files: what the parameters stand for and how/where to change them if needed. First, all file formats are explained. Section Force-field files describes the organization of the files in each force field.
Note: if you construct your own topologies, we encourage you to upload them to our topology archive at our webpage! Just imagine how thankful you’d have been if your topology had been available there before you started. The same goes for new force fields or modified versions of the standard force fields - contribute them to the force field archive!