The $protocol block

The $protocol block sets up a protocol. 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 for the protocol.
type	string	The type of the protocol (see Protocols).
system	object reference	The name of the system with which the protocol is associated.	Depends on the system to which it refers.
coords	object reference	The name of the coordinates with which the protocol is associated.	Depends on the coordinates to which it refers.

Type gmx

Parameter	Value Type	Description	Remarks
mdps	List[path]	The list of file paths of the input-parameter files (extension .mdp) for each step of the simulation workflow.
maxsteps	numerical	(Mergeable) The maximum number of steps allowed for the length of the production run.
minfactor	numerical	(Mergeable) (Optional) Controls the minimum value allowed for the updated length of a simulation that has been extended (see simulation extensions; default is 1.1).

Type gmx_alchemical

Parameter	Value Type	Description	Remarks
mdps	List[path]	The list of file paths of the template input-parameter files (extension .mdp) for each step of the simulation workflow.
maxsteps	numerical	(Mergeable) The maximum number of steps allowed for the length of the production runs.
minfactor	numerical	(Mergeable) (Optional) Controls the minimum value allowed for the updated length of a simulation that has been extended (see simulation extensions; default is 1.1).

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.