Jargons

Below shows definitions that are specific to DL_FIELD. Take some time to read them. This will make it easier for you to understand how DL_FIELD works.

• MOLECULE - also refers as the MOLECULE template, it is a pre-defined entity consists of a collection of particles which can be normal atoms, pseudo-points, atoms with core-shell components, or even united atoms and coarse-grain particles. It is usually defined in the library files using the MOLECULE and END MOLECULE directive.

• MOLECULE_TYPE - The name of a MOLECULE, often in a human-readable form.

• MOLECULE_KEY - The corresponding unique code (up to four characters) for a MOLECULE_TYPE. This is equivalent to the amino acid residue code. For example, ALA refers to alanine residue and this is alanine MOLECULE_KEY within the DL_FIELD context.

• ATOM_TYPE - The name of an atom, often in a human-readable form. An element can have different ATOM_TYPEs, which depend on its chemical environment within a molecule.

• ATOM_KEY - The corresponding code or symbol for an ATOM_TYPE. It is used within DL_FIELD to choose the appropirate potential parameters. ATOM_KEYs are also the labels used in the DL_POLY’s CONFIG and FIELD files.

• ATOM_LABEL - The unique label of a particle, use only to define a MOLECULE template. In other words, ATOM_LABELs are only visible within the MOLECULE and END MOLECULE directive.

• Potential scheme - also called the force field (FF) scheme. It refers to a force field data set in the lib/ directory. The data sets are given names to identify them. For example CHARMM, AMBER, etc.

• DL_F Notation - The DL_FIELD standard ATOM_TYPE notation for a number of FF schemes implemented within DL_FIELD. It is the universal ATOM_TYPEs of which the FF schemes share the common ATOM_TYPEs and ATOM_KEYs and the Notation directly indicates the chemical nature of the atoms in a molecular system.

• The .sf and .par files - These are called the structure file and parameter file, respectively. They are FF library files located in the lib/ directory. Each potential scheme consists of a .sf and a .par file and possibly some other supplementary files. MOLECULE template and ATOM_TYPEs definitions with the corresponding ATOM_KEYs are located in the .sf file. The .par file stores all the parameters of various interaction components such as bond interactions, angle interactions, etc.

• User-defined force field (udff) file - a user-created file that contain user-define force field information such as MOLECULE templates and FF parameters. If any of such information is also contained in the corresponding .sf or the .par files, it will be overrided and DL_FIELD will choose the information in the udff file, rather than in the library files.

• Molecular Group - also called the Molecule Group, it is a name or label given to a group of atoms or molecules in a molecular system. This is a convenient way to differentiate different class of molecules. For instance, solute molecules can be grouped in a different Molecular Group from that of solvent molecules. The Molecular Group names will appear as the molecules directive in DL_POLY’s FIELD file.