Structures and operations

This page illustrates the software structural aspects and provide brief summary how it works.

File structures

DL_FIELD package comes with the following file components:

• DL_FIELD program source in the source/ directory.
  
  
• Data library files in the lib/ directory. This is the master library that contains force field data for all available FF schemes.
  
  Each FF scheme consists of the following components:
  - Molecular structure file, with filename ends with the extension .sf.
  - Potential parameter file, with filename ends with the extention .par.
  - Other supplementary files depending on the FF schemes.
  
  The lib/ directory also contains the following files:
  - The DL_F Notation data file, DLF_Notation.
  - Atom type conversion data file, dl_field.atom.
  
  
• DL_FIELD control file.
  
  
• Solvent templates, in the solvent/ directory.
  
  
• A collection of utility program scripts, in the utility/ directory.
  
  
• The output/ directory. This is where the DLPOLY’s FIELD and CONFIG files will be produced.
  
  
• Some example structures, in the Examples/ directory.
  
  
• The control_files/ directory, which contains a collection of DL_FIELD’s control files that read the molecular strucutres in the Examples/ directory.
  
  
• The dl_f_path file, that specifies the directory paths of various file components, relative to the DL_FIELD home directory. The location and filename of the DL_FIELD control file is also specified here. The home directory is the directory path where the DL_FIELD executable file, dl_field.exe, is located. The dl_f_path and dl_field.exe must always locate in the same directory path.

Operations

Diagram below shows schematically how to run DL_FIELD.

Firstly, you would need to supply an input configuration file, in PDB, mol2 or xyz format. Then, choose a suitable FF scheme and select other options to produce a desire FF model. These are all operated within a DL_FIELD control file. After that, run DL_FIELD and it will produce the corresponding dl_poly.CONFIG and dl_poly.FIELD files in the output/ directory, which can be renamed as CONFIG and FIELD files, respectively for DL_POLY runs.

If the option (from a DL_FIELD control file) to produce Gromacs FF files is also switched on, then the corresponding gromacs.itp, gromacs.gro, gromacs.top and gromacs.mdp files will also produce.

DL_FIELD operates by using a set of simple directives, instead of using some kind of scripting language. These directives will be indicated in CAPITAL ITALICS. Optional directives will be enclosed in [SQUARE BRACKETS].

DL_FIELD jargons will be indicated in Capital Letters. Some DL_FIELD-specific notations will also be described in ALL CAPITAL LETTERS. A list of expressions can be found in the document Jargons.

If you wish to have a quick taste how DL_FIELD operates, go to this page - Ready, get set, go.

Program execution

The steps below show what happens when DL_FIELD is run:

1. Read dl_f_path.
2. Read DL_FIELD control file.
3. Read configuration (input) file.
4. Carry out atom_typing procedures to obtain ATOM_TYPEs for each atom in the system. Each ATOM_TYPE is uniquely referenced to an ATOM_KEY, as defined in the sf file.

DL_FIELD will use the following typing approaches, depending on the FF schemes and input file format:

• Template matching - Looking for suitable MOLECULE templates in sf data files (for PDB input files).
• Molecular topology analysis (for xyz and mol2 input files).
• Combination of both (for xyz input files).

5. Base on the ATOM_KEYs assigned to the atoms to determine force field parameters. This is carried out by searching for a matching set of ATOM_KEYs for a given interaction component against the parameter list in the udff or par file.
6. Produce dl_poly.CONFIG, dl_poly.FIELD and dl_poly.CONTROL files.

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