Coordinates

This page describes the implemented routines for constructing initial configurations for the simulations. These routines are of three types. The first one involves those that do not require the manipulation of particle positions and thus are program- and file-format-agnostic. They typically involve using an existing configuration without applying any modifications to it. The routines of this type provided by gmak are described in Configuration-recycling Routines.

The second type involves routines that construct a configuration from scratch, starting from the molecular geometries, box dimensions and geometrical constraints. In this context, gmak provides a number of routines that rely on GROMACS utilities to create and manipulate configurations. They encompass the construction of configuration types commonly used in force-field development. These routines are described in Configuration-construction Routines.

Finally, there are also mixed-type routines, which involve recycling an existing configuration and modifying it to suit a given need. The single routine of this type provided by gmak also relies on GROMACS utilities to carry out the configuration manipulation. It is described in Mixed-type Routines.

Configuration-recycling Routines

Arbitrary Configuration

The arbitrary-configuration routine recycles an existing configuration file. It is identified with the type any in the input file. It requires as input parameters:

coords

The path of the recycled configuration file.

Note

The arbitrary-configuration routine should be used for configurations for gas-phase simulations. For this reason, it is also provided as the alias type gmx_gas. In this case, the recycled configuration should contain a single molecule in vacuum.

Protocol-based Configuration

The protocol-based configuration routine recycles the last frame of the production run of a simulation protocol. For custom protocols, this is the configuration file returned by the function get_last_frame(). For GROMACS-based general protocols, this is the .gro file written by mdrun at the end of the production run. This routine is identified with the type follow in the input file. It requires as input parameters:

follow

The name of the protocol from which the recycled configuration is retrieved.

Configuration-construction Routines

Pure-liquid Configuration

The pure-liquid configuration routine constructs a configuration containing a given number of copies of a molecule within a box with some given dimensions. It is identified with the type gmx_liquid in the input file. It requires as input parameters:

coords

The path of a configuration file containing a single copy of the desired molecule.

nmols

The desired number of molecules.

box

The desired box dimensions. Only rectangular boxes are supported. This is either a triple of numbers specifying the box-edge lengths of a rectangular box or a single number specifying the box-edge lenghts of a cubic box.

It relies on the gmx programs:

insert-molecules

To construct the configuration based on the data supplied as input parameters.

Solute-in-solvent Configuration

The solute-in-solvent configuration routine constructs a configuration contanining given numbers of copies of two molecules (a solute and a solvent) within a box with some given dimensions. It is identified with the type gmx_solvation in the input file. It requires as input parameters:

coords

A pair of configuration-file paths. The first configuration should contain a single copy of the solute molecule. The second configuration should contain a single copy of the solvent molecule.

nmols

A pair of integers specifying the desired number of solute and solvent molecules, respectively.

box

The desired box dimensions. Only rectangular boxes are supported. This is either a triple of numbers specifying the box-edge lengths of a rectangular box or a single number specifying the box-edge lenghts of a cubic box.

It relies on the gmx programs:

insert-molecules

To create a temporary pure-liquid configuration containing the solvent molecules and also to subsequently insert the solute molecules in it, yielding the final configuration.

Slab Configuration

The slab-configuration routine constructs a configuration containing a rectangular pure-liquid slab of given dimensions within a larger rectangular box. The simulation-box dimensions are the same as those for the slab, except for one axis which is extended by a given factor, thereby creating two liquid-vacuum interfaces (see Fig. 1). It is identified with the type gmx_slab in the input file.

Fig. 1: Example of a slab configuration where the \(z\) axis of the slab has been extended by a factor of \(k\) to construct the simulation box. The figure represents only the \(yz\) plane.

It is based on the input parameters:

coords

The path of a configuration file containing a single copy of the desired molecule.

nmols

The desired number of molecules.

box

The dimensions of the pure-liquid slab (e.g., \(L_x\), \(L_y\) and \(L_z\) in Fig. 1). Only rectangular boxes are supported. This is either a triple of numbers specifying the box-edge lengths of a rectangular box or a single number specifying the box-edge lenghts of a cubic box.

axis

(optional, default is z) The axis extended in preparing the simulation box (e.g., z in Fig. 1). Possible values are x, y or z.

factor

(optional, default is 5.0) The factor by which the length of the extended axis is multiplied (e.g., k in Fig. 1).

It relies on the gmx programs:

insert-molecules

To create a temporary pure-liquid configuration with the slab dimensions.

trjconv

To create a second temporary pure-liquid configuration where it is guaranteed that no molecules are broken across the box boundaries (option -pbc whole).

editconf

To modify the length of the extended axis.

Mixed-type Routines

Slab-from-Liquid Configuration

The slab-from-liquid configuration routine constructs a slab configuration as in Slab Configuration, but starting from a pure-liquid configuration recycled from a simulation protocol, as in Protocol-based Configuration. It is identified with the type gmx_slab_follow in the input file. It is based on the input parameters:

follow

The name of the protocol from which the recycled pure-liquid configuration is retrieved.

axis

(optional, default is z) The axis extended in preparing the simulation box (e.g., z in Fig. 1). Possible values are x, y or z.

factor

(optional, default is 5.0) The factor by which the length of the extended axis is multiplied (e.g., k in Fig. 1).

It relies on the gmx programs:

trjconv

To fix any possible molecules that are broken across the box boundaries in the recycled pure-liquid configuration (option -pbc whole).

editconf

To modify the length of the extended axis.