A Guide to Preparing Input Files

The CONFIG file and the FIELD file can be quite large and unwieldy particularly if a polymer or biological molecule is involved in the simulation. This section outlines the paths to follow when trying to construct files for such systems. The description of the force field in Chapter Force Fields is essential reading. The various utility routines mentioned in this section are described in greater detail in the User Manual. Many of these have been incorporated into the DL_POLY GUI 99 and may be conveniently used from there.

Inorganic Materials

The utility genlat can be used to construct the CONFIG file for relatively simple lattice structures. Input is interactive. The FIELD file for such systems are normally small and can be constructed by hand. Otherwise, the input of force field data for crystalline systems is particularly simple, if no angular forces are required (notable exceptions to this are zeolites and silicate glasses - see below). Such systems require only the specification of the atomic types and the necessary pair forces. The reader is referred to the description of the DL_POLY_4 FIELD file for further details (Section:ref:The FIELD File<field-file>).

DL_POLY_4 can simulate zeolites and silicate (or other) glasses. Both these materials require the use of angular forces to describe the local structure correctly. In both cases the angular terms are included as three-body terms, the forms of which are described in Chapter Force Fields. These terms are entered into the FIELD file with the pair potentials.

An alternative way of handling zeolites is to treat the zeolite framework as a kind of macromolecule (see below). Specifying all this is tedious and is best done computationally: what is required is to determine the nearest image neighbours of all atoms and assign appropriate bond and valence angle potentials. What must be avoided at all costs is specifying the angle potentials without specifying bond potentials. In this case will automatically cancel the non-bonded forces between atoms linked via valence angles and the system will collapse. The advantage of this method is that the calculation is likely to be faster than using three-body forces. This method is not recommended for amorphous systems.

Macromolecules

To set up force fields for macromolecules, or indeed any covalent molecules, it is best to use DL_FIELD - http://www.ccp5.ac.uk/DL_FIELD/. It is a program application tool developed to facilitate the construction of force field models for biological molecules and other molecules with complex geometries. For instance proteins, carbohydrates, polymers and networked molecules such as graphenes and organic cages. Although created to assist , is a separate program suite that requires separate registration!

The primary functions of DL-FIELD are as follows:

  1. Force field model converter: DL_FIELD converts the user’s atom models, supplied in PDB file format, into input files that are recognisable and ready to run with and DL_POLY_4 programs with minimum user’s intervention. This basically involves the conversion of the user’s atomic configuration in simple xyz coordinates into identifiable atom types base on a particular user-selectable potential schemes and then automatically generate the DL_POLY configuration file (CONFIG), the force field file (FIELD) and a generic control file (CONTROL).

  2. Force field editor: DL_FIELD allows the user to edit or modify parameters of a particular force field scheme in order to produce a customised scheme that is specific to a particular simulation model. In addition, the standard force field model framework can also be easily modified. For instance, introduction of pseudo points and rigid body implementation to an otherwise standard potential scheme such as CHARMM or AMBER, etc.

  3. Force field library repertoire: DL_FIELD contains a range of popular potential schemes (see below), all described in a single DL_FIELD format that are also easily recognisable by the user for maintenance purposes. Users can easily expand the existing library to include other new molecules.

Force Field Schemes

The available force field schemes are as follows:

CHARMM - proteins, ethers, some lipids and carbohydrates.

AMBER - proteins and Glycam for carbohydrates.

OPLSAA - proteins

DREIDING - General force field for covalent molecules.

PCFF - Polyorganics and other covalent molecules.

Model Construction

DL_FIELD does not have feature to construct molecular models. This can be achieved by either using DL_POLY GUI 99 or any other standard molecular building packages. The output files must be converted into the PDB format. In the case of proteins, these structures are usually obtained from data banks such as PDB. These ‘raw PBD’ files must first be preprocessed by the user before they are in a ‘readable format’ for DL_FIELD. To ensure this, it is advisable that users take into consideration the following steps:

  1. Decide on inclusion/exclusion of and if necessary manually delete molecular residues that involve multiple occupancies in crystalline structures.

  2. Usually, hydrogen atoms are not assigned in the raw PDB file. The molecules must therefore be pre-filled with hydrogen atoms (protonated) by using any standard packages available. The user must ensure that proper care is taken of terminal residues which must also be appropriately terminated.

  3. Decide on the various charge states of some amino acids, such as histidine (HIS), lysine (LYS), glutamic acid (GLU), etc., by adding or deleting the appropriate hydrogen atoms. Force field schemes such as CHARMM will have different three-letter notations for amino acids of different charge states, DL_FIELD will automatically identify these differences and assign the appropriate potential parameters accordingly.

  4. For cysteine (CYS) molecules with disulphide bonds, thiolate hydrogen atoms must be removed. DL_FIELD will automatically define disulphide bonds between the molecules, provided the S-S distance is within a ‘sensible’ value.

  5. DL_FIELD does not solvate the molecules and it is the user’s responsibility to add water by using any standard package available (for example the DL_POLY GUI 99).

Fore more details or further information, please consult the DL_FIELD manual and website. http://www.ccp5.ac.uk/DL_FIELD/

Adding Solvent to a Structure

The utility wateradd adds water from an equilibrated configuration of 256 SPC water molecules at 300 K to fill out the MD cell. The utility solvadd fills out the MD box with single-site solvent molecules from a fcc lattice. The FIELD files will then need to be edited to account for the solvent molecules added to the file.

Hint: to save yourself some work in entering the non-bonded interactions variables involving solvent sites to the FIELD file put two bogus atoms of each solvent type at the end of the CONNECT_DAT file (for AMBER force field`s) the utility ``ambforce` will then evaluate all the non-bonded variables required by . Remember to delete the bogus entries from the CONFIG file before running .

Analysing Results

DL_POLY_4 is not designed to calculate every conceivable property you might wish from a simulation. Apart from some obvious thermodynamic quantities and radial distribution functions, it does not calculate anything beyond the atomic trajectories. You must therefore be prepared to post-process the HISTORY file if you want other information. There are some utilities in the package to help with this, but the list is far from exhaustive. In time, we hope to have many more. Our users are invited to submit code to the DL_POLY_4 public library to help with this.

The utilities available are described in the User Manual. Users should also be aware that many of these utilities are incorporated into the DL_POLY GUI 99.