Force field files for Gromacs

This feature is only available for version 4.11 onwards.

This page describes how to use DL_FIELD to produce FF files for Gromacs simulation package. It does not describe Gromacs file structure and directives in details. For more information, please consult Gromacs manual.

For more information about Gromacs output in DL_FIELD, consult the manual, Chapter 14.

../../_images/Orange_bar6.png

Option to produce Gromacs files

By default, DL_FIELD will always produce FF files for DL_POLY. To produce FF files for Gromacs as well, the keyword gromacs must be used in the DL_FIELD control file as follows:

Control file title. For DL_FIELD 4.11
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)
...
...
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
etoh  1.9 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

...
...

************* Gromacs control ******************
1            * Run Gromacs
gmx          * Gromacs executable filename
/usr/bin/ * absolute path to Gromacs
1            * MM single-point calc.
...
...

If the option to run Gromacs program is also switched on, then after FF files are produced, DL_FIELD will setup a binary tpr file and run a single-point calculation on Gromacs (provided the program is also available in the same machine where DL_FIELD is executed).

../../_images/Orange_bar6.png

Output files

Upon successful FF conversions, DL_FIELD will produce the following files:

  1. The system topology file, gromacs.top.
  2. One or more include topology files, gromacsX.itp, wwhere X = 1, 2, 3, …
  3. A coordinate file, gromacs.top.
  4. A generic MD parameter file, gromacs.mdp.

DL_FIELD can produce several itp files, which correspond to the number of Molecular Groups defined in the configuration file.

Each itp file contains force field information for each Molecular Group. These itp files are included in the top file, which defines the ATOM_TYPEs and provides a summary of system composition.

^ GO TO TOP ^