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:
Read dl_f_path.
Read DL_FIELD control file.
Read configuration (input) file.
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).
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.
Produce dl_poly.CONFIG, dl_poly.FIELD and dl_poly.CONTROL files.