Getting Started#
Welcome to the Getting Started guide!
Contents#
This tutorial will walk you through the basics of the DL_FIELD file formats and how to assign forcefield parameters to an example system. Before getting started, you should register to use the software here.
After downloading the source code, instructions on how to unpack and general guidance can be found here. A brief summary of key DL_FIELD files is provided below.
Our beginner-friendly tutorials assume you are working from the dl_f_4.XX/ (e.g. dl_f_4.12/, version dependent) directory that is created upon unpacking the source code. This directory contains dl_field.control (DL_FIELD CONTROL file) which controls how input molecular systems are parameterised, for example by defining the forcefield. A breakdown of the structure and available features of the control file is provided in DL_FIELD control file.
The paths to the CONTROL file, forcefield library files and output files (amoung others) are located in the dl_f_path file. The paths are defined relative to the DL_FIELD home directory (dl_f_4.XX/), which users should consider when making changes.
Upon compiling the source code, the DL_FIELD executable (dl_field) can be used to run the software from the command line with
$ ./dl_field
Note
The dl_f_path file must be located in the same directory as the dl_field executable.
Successful structure conversions result in output files written to the directory specified in dl_f_path (/output by default). For example, the GROMACS .mdp, .top and .gro input files or DL_POLY/LAMMPS equivalents. For further details, consult the general guidance page, reference manual, or the tutorials in this series.
DL_FIELD control file#
The DL_FIELD CONTROL file contains a set of control options for all the operations DL_FIELD provides. Below is an example file where we highlight key directives and things to consider in order to run DL_FIELD on a basic system. For more detailed information, visit this page.
An example CONTROL file is shown below
Control file title. For DL_FIELD 4.10
1 * Construct DL_POLY output files
gromacs * Seconday output files (gromacs, 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
PE.xyz * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
0 0.1 mol/dm^3 15.0 * Solution Maker: on/off, density, unit, cutoff)
0 * 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
1 * Epsilon mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
2 * Sigma mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
1 * Epsilon mixing rule (BETWEEN different FF) : 1 = geometric 2 = arithmatic
2 * 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
0 * 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 (see below)
120.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 120.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 120.0 * 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.
1 * Position solute at origin? 1 = yes, 0=no
none 1.9 default * Solvate model? none or specify solvent (see below), distance criteria and FF.
0 10.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute
0 * Not use
0 * Not use
0 * Not use
************* DL_POLY control ******************
0 * Run DL_POLY program
DLPOLY.Z * DL_POLY executable filename
/home/usr/ * absolute path to DL_POLY program
4 * Number of processors (mpirun)
1 * MM calculation 1=on 0=off
0 1000 * Structural Relaxation level (0 - off, 1,2 or 3). Total timestep
8.0 * cutoff (vdw and electrostatic)
100000 * Time limit for DL_POLY run (in seconds)
************* Gromacs control ******************
0 * Run Gromacs
gmx * Gromacs executable filename
/usr/bin/gmx * absolute path to Gromacs
0 * MM single-point calc.
************* Lammps control ******************
0 * Run Lammps
lmp * Lammps executable filename
/usr/bin/ * absolute path to Lammps
1 * MM single-point calc.
########################################################
Atom state specification: type Molecular_Group filter [value]
FREEZE ORG1 cp
FREEZE ORG2 CT
RIGID A
TETHER CLY st 100.0
CONSTRAIN SOD1 h-bond
#########################################################
Please do not remove those '####' lines.
All select atom commands must be included within the two '####' lines
Some remarks...
...
...
...
Note
Comments in the control file are specified with the * character.
Note
The order of the control settings is fixed and must not be removed nor rearranged.
Highlighted are key control options required to run a successful DL_FIELD operation. The first two specify the format of the output files DL_FIELD creates. The Molecular Dynamics packages DL_POLY, GROMACS and LAMMPS are currently supported, along with ChemShell for QM/MM. DL_FIELD always produces DL_POLY files (first line), whereas the second line specifies the format of secondary output files.
The third highlighted line provides the forcefield used for the parameter assignment. For a list of available forcefields, consult the reference manual.
The final line highlighted is how users can specify the path to their input structure. DL_field currently supports the PDB, xyz and mol2 file formats. For more information on how to ensure DL_field can read your input structure properly, visit this page.
The other operations in the CONTROL file may be changed according to specific user or forcefield requirements. The tutorials in this series provide examples of this for various systems.
DL_FIELD path file#
As mentioned previously, the dl_f_path file contains the relative paths to the CONTROL file, output files and solvent templates, amoungst others (see here. You must not use absolute paths. An example file is printed below:
# Directory paths for DL_FIELD version 4.10.
# C W Yong, January 2024
# paths
library = lib/
solvent = solvent/
output = output/
# Control file
control = tutorial_confs/dl_field.control
##########################
# optional files
# Look for CHARMM rtf, and or prm files
# See Chapters 13.3 and 13.4
# charmm_rtf = pentanoic_acid.rtf OPLS2005
# charmm_prm = pentanoic_acid.prm OPLS2005
# charmm_psf = example.psf charmm36_prot
# charmm_pdb = example.pdb charmm36_prot
During the tutorials, change the CONTROL file path as required.
Setting up the tutorials#
To keep track of the tutorial material, create the following two directories in dl_f_4.XX/.
$ mkdir tutorial_confs
$ mkdir tutorial_controls
Here we will place the input molecule configuration files and corresponding CONTROL file for each tutorial. An example control file should already be located in dl_f_4.XX/, which we can copy to tutorial_controls/.
Finally, we need to update dl_f_path with the new CONTROL file location. Comment out the old location and add the highlighted line.
# control = dl_field.control # old location
control = tutorial_controls/dl_field.control # new location
The file name can be modified from the default dl_field.control as required.