A force field is built up from two distinct components:
The set of equations (called the potential functions) used to generate the potential energies and their derivatives, the forces. These are described in detail in the previous chapter.
The parameters used in this set of equations. These are not given in this manual, but in the data files corresponding to your GROMACS distribution.
Within one set of equations various sets of parameters can be used. Care must be taken that the combination of equations and parameters form a consistent set. It is in general dangerous to make ad hoc changes in a subset of parameters, because the various contributions to the total force are usually interdependent. This means in principle that every change should be documented, verified by comparison to experimental data and published in a peer-reviewed journal before it can be used.
GROMACS 2023.1 includes several force fields, and additional ones are available on the website. If you do not know which one to select we recommend GROMOS-96 for united-atom setups and OPLS-AA/L for all-atom parameters. That said, we describe the available options in some detail.
All-hydrogen force field#
The GROMOS-87-based all-hydrogen force field is almost identical to the normal GROMOS-87 force field, since the extra hydrogens have no Lennard-Jones interaction and zero charge. The only differences are in the bond angle and improper dihedral angle terms. This force field is only useful when you need the exact hydrogen positions, for instance for distance restraints derived from NMR measurements. When citing this force field please read the previous paragraph.
GROMACS supports the GROMOS-96 force fields 77. All parameters for the 43A1, 43A2 (development, improved alkane dihedrals), 45A3, 53A5, and 53A6 parameter sets are included. All standard building blocks are included and topologies can be built automatically by pdb2gmx.
The GROMOS-96 force field is a further development of the GROMOS-87 force field. It has improvements over the GROMOS-87 force field for proteins and small molecules. Note that the sugar parameters present in 53A6 do correspond to those published in 2004110, which are different from those present in 45A4, which is not included in GROMACS at this time. The 45A4 parameter set corresponds to a later revision of these parameters. The GROMOS-96 force field is not, however, recommended for use with long alkanes and lipids. The GROMOS-96 force field differs from the GROMOS-87 force field in a few respects:
the force field parameters
the parameters for the bonded interactions are not linked to atom types
a fourth power bond stretching potential (Fourth power potential)
an angle potential based on the cosine of the angle (Cosine based angle potential)
There are two differences in implementation between GROMACS and GROMOS-96 which can lead to slightly different results when simulating the same system with both packages:
in GROMOS-96 neighbor searching for solvents is performed on the first atom of the solvent molecule. This is not implemented in GROMACS, but the difference with searching by centers of charge groups is very small
the virial in GROMOS-96 is molecule-based. This is not implemented in GROMACS, which uses atomic virials
The GROMOS-96 force field was parameterized with a Lennard-Jones cut-off
of 1.4 nm, so be sure to use a Lennard-Jones cut-off
rvdw) of at least 1.4. A larger cut-off is possible
because the Lennard-Jones potential and forces are almost zero beyond
GROMACS can read and write GROMOS-96 coordinate and trajectory files. These files should have the extension g96. Such a file can be a GROMOS-96 initial/final configuration file, a coordinate trajectory file, or a combination of both. The file is fixed format; all floats are written as 15.9, and as such, files can get huge. GROMACS supports the following data blocks in the given order:
TIMESTEP (optional) POSITION/POSITIONRED (mandatory) VELOCITY/VELOCITYRED (optional) BOX (optional)
See the GROMOS-96 manual 77 for a complete description of the blocks. Note that all GROMACS programs can read compressed (.Z) or gzipped (.gz) files.
GROMACS provides native support for the following AMBER force fields:
GROMACS supports the CHARMM force field for proteins 118, 119, lipids 120 and nucleic acids 121, 122. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested – both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with GROMACS-specific techniques such as virtual sites (enabling long time steps) recently implemented 123 – and the details and results are presented in the paper by Bjelkmar et al. 124. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
When selecting the CHARMM force field in
pdb2gmx the default option
is to use CMAP (for torsional correction map).
To exclude CMAP, use
-nocmap. The basic form of the CMAP
term implemented in GROMACS is a function of the \(\phi\) and
\(\psi\) backbone torsion angles. This term is defined in the
rtp file by a
[ cmap ] statement at the
end of each residue supporting CMAP. The following five atom names
define the two torsional angles. Atoms 1-4 define \(\phi\), and
atoms 2-5 define \(\psi\). The corresponding atom types are then
matched to the correct CMAP type in the
that contains the correction maps.
A port of the CHARMM36 force field for use with GROMACS is also available at the MacKerell lab webpage.
Coarse-grained force fields#
Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. To achieve this, typically whole groups of atoms are represented by single beads and the coarse-grained force fields describes their effective interactions. Depending on the choice of parameterization, the functional form of such an interaction can be complicated and often tabulated potentials are used.
Coarse-grained models are designed to reproduce certain properties of a reference system. This can be either a full atomistic model or even experimental data. Depending on the properties to reproduce there are different methods to derive such force fields. An incomplete list of methods is given below:
Conserving free energies
MARTINI force field (see next section)
Conserving distributions (like the radial distribution function), so-called structure-based coarse-graining
(iterative) Boltzmann inversion
Inverse Monte Carlo
Note that coarse-grained potentials are state dependent (e.g. temperature, density,…) and should be re-parametrized depending on the system of interest and the simulation conditions. This can for example be done using the Versatile Object-oriented Toolkit for Coarse-Graining Applications (VOTCA) (???). The package was designed to assists in systematic coarse-graining, provides implementations for most of the algorithms mentioned above and has a well tested interface to GROMACS. It is available as open source and further information can be found at www.votca.org.
The MARTINI force field is a coarse-grain parameter set that allows for the construction of many systems, including proteins and membranes.
The PLUM force field 126 is an example of a solvent-free protein-membrane model for which the membrane was derived from structure-based coarse-graining 127. A GROMACS implementation can be found at github.com/tbereau/plumx.