Gromacs setting and restrictions

Gromacs contains numerous directives and different ways to achieve same FF definitions. In addition, not all the features implemented in DL_FIELD is applicable to Gromacs.

This page describes some default rules and restrictions when setting up FF files for Gromacs.

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Default settings

DL_FIELD adopts the following default rules:

  1. The nrexcl parameter is always set to 3. This means non-bonded interactions (vdw and Coulombic) on the 1-2, 1-3 and 1-4 atom pairs will be excluded by default.
  2. The gen-pair parameter is always set to no. This instructs Gromacs not to automatically generate 1-4 atom pairs for non-bonded interactions.
  3. The fudge QQ (1-4 Coulombic scaling factor) and fudge LJ (1-4 vdw scaling factor) defined in the [ defaults ] Gromacs directive will be set to the chosen FF scheme. These scaling factors are only shown as a reference. For a multiple-potential setting, they are set to a default value of 1.0. In both cases, they are most probably not going to be used because the correct scaling factors are defined in the [ pair ] directive (see below).
  4. All 1-4 interactions, their scalings or specific potential parameters, will be explicitly defined under the [ pair ] Gromacs directive. If require, this is where any additional non-bonded interactions that has been excluded due to the nrexcl value will be defined.
  5. All other non-bonded interactions (1-5 and beyond) will be mixed according to the combination rule set in the [ default ] directive. The vdw parameters and charges for these calculations will be extracted from the [ atomtypes ] and [ atoms ] Gromacs directives, respectively.
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Restrictions

  1. At the moment, conversion to Gromacs files only works for input configurations expressed in PDB and xyz formats only.
  2. Irrespective of what energy unit is specified in DL_FIELD control file, all energy unit will be converted to kJ/mol and nm for the unit distance in the Gromacs files.
  3. FF conversions only work for FF schemes that use LJ 12-6 and Buckingham potentials. For example, PCFF that uses LJ 9-6 form would not work. In addition, Buckingham potentials only work for older version Gromacs (before 2019 versions).
  4. Gromacs imposes a fix-format on the gromacs.gro coordinate files. For instance, the atom labels can only display up to five-character in length and the coordinates are specified to three decimals. An error can occur when running Gromacs if the data format is violated.However, DL_FIELD will not check for this.
  5. Because of point (3), comparison of single-point energies between DL_POLY and Gromacs are likely to be different due to differing scaling precisions and distance units being used.
  6. DL_FIELD does not include CMAP energy correction for the φ/ψ backbone dihedral angles. Therefore, it is not recommended to use DL_FIELD to setup protein force fields such as CHARMM that use CMAP for molecular simulations.
  7. For multiple-potential models, only systems based on Lennard-Jones 12-6 functions can be successfully setup. Gromacs does not support mixed-function setting. For example, a model consists of both Lennard-Jones and Buckingham potentials for the vdw interactions. DL_FIELD can still produce Gromacs files for such systems, although grompp will generate an error when trying to produce a tpr file.
  8. The rigid body or the [RIGID] directive in DL_FIELD, is not supported for Gromacs. The exception would be for the water models. In this case, the Gromacs directive command [ settles ] will be used.

For more details about the restrictions, please consult Chapter 14.3 of DL_FIELD manual.

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