Systems and Topologies

In gmak, defining a system type means specifying how to write a topology file, given

• the interaction-parameter objects (see Interaction Parameters)

• additional data given in the input file in the form of input parameters.

gmak provides a system type suitable for use with the GROMACS software package—the gmx system type, described below.

For flexibility, gmak also provides a function in the customization API that allows one to define a custom system type—either suitable for GROMACS or for other simulation packages.

GROMACS-compatible Systems

Template Topology

The gmx system type requires the path of a topology file with extension .top to be provided as an input parameter named template. This file works as a template, where the values of the interaction parameters modified by gmak are replaced for at each grid point.

Note

When the template topology is read, all #include directives are expanded and replaced by the contents of the corresponding file. If the directive does not point to an absolute path, gmak looks for it recursively in the local directory and in the GROMACS library directory as inferred from the path of the gmx binary or the GMXLIB environment variable.

Replacement of Interaction Parameters

The replacement of the values of the interaction parameters in a template is carried out recursively. This means that each interaction parameter \(I_n\) is replaced for in a template \(T_{n-1}\) that results from replacing the previous parameter \(I_{n-1}\) on a previous template \(T_{n-2}\), and so on. The starting point \(T_0\) is, of course, the template file provided as an input parameter in the input file. Schematically:

\[T_0 \xrightarrow{I_1} T_1 \xrightarrow{I_2} T_2 \xrightarrow{I_3} \ldots T_{n-1} \xrightarrow{I_n} T_n\]

The handling of the interaction parameters for the gmx system type is described below.

Lennard-Jones Parameters

Atomtypes

The values of atomtype interaction parameters are replaced for in a template by substituing them for the values of the corresponding atomtype parameters inside the [ atomtypes ] directive. The original template values are stored for further use.

After that, the standard pairs inside the [ nonbond_params ] directives are scanned and those that derive from the atomtype based on the inclusion/exclusion regular-expression rules explained in Atomtype Parameters have their interaction-parameter values scaled to reflect the change in the parameters of the atomtype.

The value of the scaling factor depends on

• the Lennard-Jones potential representation (\(C_6\)-\(C_{12}\) or \(\sigma\)-\(\epsilon\))

• the combination rule

• the type of the parameter in the context of the Lennard-Jones potential (\(C_6/\sigma\) or \(C_{12}/\epsilon\))

In GROMACS, the Lennard-Jones representation and the combination rule are tied together and chosen in the [ defaults ] directive of the topology. Using \(\alpha\) to denote the type of the interaction parameter being adjusted in the context of the Lennard-Jones potential, and \(\alpha_i\) and \(\alpha_f\) to denote the template (in the recursive sense described above) and target values, respectively, the scaling factor \(f\) is given by

\[f = 1 + \frac{1}{2}\left(\frac{\alpha_f}{\alpha_i} - 1 \right)\]

for \(\alpha \equiv \sigma\) and combination rule 2, and

\[f = \sqrt{\alpha_f/\alpha_i}\]

for all other cases.

Note

We highly encourage reading the parameter-files section of the GROMACS user guide for more information on the combination rules.

Standard Pairtypes

The values of standard-pairtype interaction parameters are replaced for in a template by substituting them for the values of the corresponding standard-pairtype parameters inside the [ nonbond_params ] directive.

1,4 Pairtypes

The values of 1,4-pairtype interaction parameters are replaced for in a template by substituting them for the values of the corresponding 1,4-pairtype parameters inside the [ pairtypes ] directive.

Warning

Under no circumstances will gmak add a parameter type to the template file—it only modifies the values of existing parameter types.

Macro-based Parameters

The values of macro-based interaction parameters are replaced for in a template by replacing every instance of the interaction-parameter name (a string token) by the interaction-parameter value.

Custom Parameters

The values of custom interaction parameters are replaced for in a template by relying on a user-implemented function (see Systems in the customization API).