The expression MOLECULE is a DL_FIELD-specific jargon. It is a pre-define entity consists of a collection of particles. In most cases, a MOLECULE consists of a group of atoms that made up a molecule. However, it can also include pseudo-points, atoms with core-shell components, or even united atoms and coarse-grain particles. In DL_FIELD, members that made up a MOLECULE are called ATOMs.

MOLECULEs are defined in sf files. A MOLECULE is always defined and enclosed within the MOLECULE and END MOLECULE directives. MOLECULEs are also called the molecular templates. In some FF schemes, DL_FIELD will look for suitable molecular templates that match with the user's system input files.

For example, for a PDB protein file, DL_FIELD will read the residue information in the file and then look for the matching templates in the sf file. Close