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.