# nwARGOS topology

The static information about a molecular system that is needed for a molecular simulation is provided to the simulation module in a topology file (top). Items in this file include, among many other things, a list of atoms, their non-bonded parameters for van der Waals and electrostatic interactions, and a complete connectivity in terms of bonds, angles and dihedrals.
In nwArgos, molecular systems are composed of solvent and solute, which are treated separately. Solvent, is a collection of identical molecules defined only once in the topology file. In the current implementation only one solvent can be defined. Everything else in the molecular system is solute. Solute is the collection of molecules in the system of which each atom is explicitly defined in the topology.
Molecular systems are defined in terms of segments. Molecules can be defined in a single segment, or as a collection of segments. Typically, repetitive parts of a molecule are each defined as a single segment. Segment files (sgm) can be quite complicated to define and are, therefore, collected in a set of database libraries. The list of segments and their connectivity that make a molecular system is defined in a sequence file (seq). A utility nwTOP reads the sequence from this file, retrieves all needed segments from the available segment databases, and generates the topology file.
Segments may not always be available in one of the existing databases. A utility nwSGM reads a rudimentary, force-field independent definition of a segment from a fragment file (frg), and constructs a template for a force-field dependent segment. Just like segments, fragments can be collected into a set of database files.

- Creating frg files
- Creating sgm files
- Creating seq files
- Creating top files