The $coordinates block

The $coordinates block sets up a routine for constructing initial configurations. This block can appear multiple times in the input file.

The input parameters that are set in this block are listed below.

Block parameters

Parameter	Value Type	Description	Remarks
name	string	The name chosen for the configuration-initialization routine.
type	string	The type of the configuration-initialization routine (see Coordinates).

Type any

Parameter	Value Type	Description	Remarks
coords	path	The path of the recycled configuration file.

Type folllow

Parameter	Value Type	Description	Remarks
follow	object reference	The name of the protocol from which the recycled configuration is retrieved.	Depends on the protocol to which it refers and on the $grid block.

Type gmx_liquid

Parameter	Value Type	Description	Remarks
coords	path	The path of a configuration file containing a single copy of the desired molecule.
nmols	numerical	The desired number of molecules.
box	List[string, numerical] OR List[string, numerical, numerical, numerical]	The type of box (cubic or rectangular) followed by the desired box dimensions (one length or a triple of lengths).

Type gmx_solvation

Parameter	Value Type	Description	Remarks
coords	List[path, path]	A pair of configuration-file paths for the solute and solvent molecules.
nmols	List[numerical, numerical]	A pair of integers specifying the desired number of solute and solvent molecules, respectively.
box	List[string, numerical] OR List[string, numerical, numerical, numerical]	The type of box (cubic or rectangular) followed by the desired box dimensions (one length or a triple of lengths).

Type gmx_slab

Parameter	Value Type	Description	Remarks
coords	path	The path of a configuration file containing a single copy of the desired molecule.
nmols	numerical	The desired number of molecules.
box	List[string, numerical] OR List[string, numerical, numerical, numerical]	The type of box (cubic or rectangular) followed by the desired box dimensions (one length or a triple of lengths).
axis	string	(Optional) The axis extended in preparing the simulation box. Possible values are x, y or z (default).
factor	numerical	(Optional) The factor by which the length of the extended axis is multiplied (default is 5.0).

Type gmx_slab_follow

Parameter	Value Type	Description	Remarks
follow	object reference	The name of the protocol from which the recycled pure-liquid configuration is retrieved.	Depends on the protocol to which it refers and on the $grid block.
factor	numerical	(Optional) The factor by which the length of the extended axis is multiplied (default is 5.0).

Note

Parameters that are not listed above can also be supplied. They are not recognized by the program in any special way, but are parsed and made available in the Customization API, together with all the other block parameters, as an InputParameters object.

Example

See Tutorial for a commented example.