Setup solutionsΒΆ
This exercise shows how to use DL_FIELD to setup a solution model by using the Solution Maker Feature.
Below lists a number of small drug molecules (solutes). They are all nosteroidal anti-flammatory drug molecules. For this exercise we will solvate these drug molecules with a solvent of your choice. The OPLS2005 FF scheme will be used to setup FF files for DL_POLY.
Procedures
Download or save one of the drug molecules as shown above into a filename that ends with .xyz, to indicate to DL_FIELD it is in xyz format. Save this in DL_FIELD home directory (where the dl_field executable file is located).
Edit DL_FIELD control file (for example, dl_field.control). Insert the correct options as highlighted below:
Solution model setup
1 * Construct DL_POLY output files
none * Secondary output files (gromacs, lammps, chemshell, or none)
opls2005 * Type of force field require (see list below for choices).
kcal/mol * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal * Conversion criteria (strict, normal, loose)
1 * Bond type (0=default, 1=harmonic , 2=Morse)
1 * Angle type (0=default, 1=harmonic, 2=harmonic cos)
none * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
mefenamic_acid.xyz * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
1 0.4 mol/dm^3 8.0 * Solution Maker: on/off, density, unit, cutoff)
1 * Optimise FIELD output size, if possible? 1=yes 0=no
2 * Atom display: 1 = DL_FIELD format. 2 = Standard format
2 * Vdw display format: 1 = 12-6 format 2 = LJ format
default * Epsilon mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
default * Sigma mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
0 * Epsilon mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
0 * Sigma mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
0 * Epsilon mixing rule (BETWEEN different FF) : 1 = geometric 2 = arithmatic
0 * Sigma mixing rule (BETWEEN different FF): 1 = geometric 2 = arithmatic
0 * Display additional info. for protein 1=Yes 0=No
0 * Freeze atoms? 1 = Yes (see below) 0 = No
0 * Tether atoms? 1 = Yes (see below) 0 = No
1 * Constrain bonds? 1 = Yes (see below) 0 = No
0 * Apply rigid body? 1 = Yes (see below) 0 = No
1 * Periodic condition ? 0=No, other number = type of box
40.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 40.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 40.0 * Cell vector c (x, y, z)
default * 1-4 scaling for coulombic (put default or x for scaling=x)
default * 1-4 scaling for vdw (put default or x for scaling=x)
0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature.
0 * Position solute at origin? 1 = yes, 0=no
etoh 1.3 default * Solvate model? none or specify solvent (see below) and distance criteria.
0 10.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute
...
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Atom state specification: type Molecular_Group filter [value]
CONSTRAIN XYZ h-bond
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...
...
The options selected will instruct DL_FIELD to setup FF models using OPLS2005 FF scheme. DL_FIELD will duplicate the number of molecule to give the solute concentration of 0.4 mol/dm^2 and each solute must be at least 8 angstrom apart from one another.
The simulation box size is 40x40x40 angstrom. The H-bond constrains are also applied for the molecules.
Once the solute is duplicated, DL_FIELD will introduce ethanol (etoh) solvent molecules, which must be at least 1.3 angstrom from solutes.
Remember to check dl_f_path is pointing to the right control file you are using.
Run DL_FIELD (./dl_field). Once successfully run, DL_FIELD will produce the following files: The dl_poly.CONFIG and dl_poly.FIELD files.
Take a look at output files (dl_field.output), which provides information about the conversion. Take a look also dlf_notation.output, which shows the atom typing information, in DL_F Notation.
Congratulations! You have just setup a solution model.
If you wish, you can proceed: Run Simulation (DL_POLY).
Otherwise, you can choose other solvents and run step (2) again. Solvent list is available in the solvent/ folder.
Note
You can also use this exercise to set up FF models for other packages such as GROMACS or LAMMPS. All you need to do is to select either gromacs or lammps in second option of the DL_FIELD control file.