The simulation section

The simulation section defines and selects the simulation PyRETIS will run.

Example Simulation section:
Simulation
----------
task = retis
steps = 20000
interfaces = [-0.9, -0.8, -0.7, -0.6, -0.5, -0.4, -0.3, 1.0]

For this section, the keyword task specifies the type of simulation to run and this will also determine the keyword that can be set in this section, but it might also require additional sections to be defined. This is given in the table below:

Table 1 Possible values for the task keyword
Task Description Keywords Required sections
retis A replica exchange transition interface sampling simulation. task, steps, interfaces tis, retis
tis A transition interface sampling simulation. task, steps, interfaces, ensemble, detect tis
md-flux A MD FLUX simulation. task, steps, interfaces  
md-nve A MD NVE simulation. task, steps  

Since the different tasks require different keyword, these are described below:

The retis task

The retis task defines a replica exchange transition interface sampling simulation.

Example Simulation section for task retis:
Simulation
----------
task = retis
steps = 20000
interfaces = [-0.9, -0.8, -0.7, -0.6, -0.5, -0.4, -0.3, 1.0]

Keywords for the retis task

For the retis task, the following keywords can be set:

Table 2 Keywords for the retis task.
Keyword Description
steps The number of retis steps to perform.
interfaces The location of the interfaces to consider.

In addition, this task requires that the sections TIS and RETIS are defined.

Keyword steps

steps = integer

The steps keyword defines the number of RETIS cycles to perform.

Default
Not any, this keyword must be specified.

Keyword interfaces

interfaces = list of floats

The interfaces keyword specifies the interfaces to use in the path simulation.

Default
Not any, this keyword must be specified.

The tis task

The tis task defines a transition interface sampling simulation.

Example Simulation section for task tis (multiple path ensembles):
Simulation
----------
task = tis
steps = 20000
interfaces = [-0.9, -0.8, -0.7, -0.6, -0.5, -0.4, -0.3, 1.0]
Example Simulation section for task tis (a single path ensemble):
Simulation
----------
task = tis
steps = 20000
interfaces = [-0.9, -0.9, 1.0]
detect = -0.8
ensemble = 1

Keywords for the tis task

For the tis task, the following keywords can be set:

Table 3 Keywords for the tis task.
Keyword Description
steps The number of steps to perform.
interfaces The interfaces defining the TIS ensemble.
ensemble For defining the ensemble considered.
detect The interface used for detecting successful paths.

In addition, this task requires that the section TIS is defined.

Keyword steps

steps = integer

The steps keyword defines the number of TIS cycles to perform.

Default
Not any, this keyword must be specified.

Keyword interfaces

interfaces = list of floats

The interfaces keyword specifies the interfaces to use in the path simulation. If the number of interfaces given are 3 or less, a single TIS simulation will be formed, otherwise input files for several single TIS simulations will be written. These simulations can then be run manually.

Default
Not any, this keyword must be specified.

Keyword ensemble

ensemble = integer

A number specifying the path ensemble we are simulating, ensemble = 1 corresponds to [0^+], 1 to [1^+] and so on. This is only needed for running a single TIS simulation.

Default
Not any, this keyword must be specified.

Keyword detect

detect = float

A number specifying the interface used for detecting successful paths. This is only needed for a single TIS simulation.

Default
Not any, this keyword must be specified.

The md-flux task

The md-flux task is a molecular dynamics simulation for determining the initial flux for a TIS path simulation.

Example Simulation section for task md-flux:
Simulation
----------
task = md-flux
steps = 10000000
interfaces = [-0.9]

Keywords for the md-flux task

For the md-flux task, the following keywords can be specified:

Table 4 Keywords for the md-flux task
Keyword Description
steps Defines the number of steps to carry out.
interfaces Defines the interfaces to consider for the flux simulation.

Keyword steps

steps = integers

The steps keyword specifies the number of MD steps to perform.

Default
Not any, this keyword must be specified.

Keyword interfaces

interfaces = list of floats

The interfaces keyword specifies for which interfaces the initial flux should be obtained. This can be given as a list of floats.

Default
Not any, this keyword must be specified.

The md-nve task

The md-nve task is a NVE molecular dynamics simulation.

Example Simulation section for task md-nve:
Simulation
----------
task = md-nve
steps = 10000000

Keywords for the md-nve task

The following keywords can be specified for the md-nve task:

Table 5 Keywords for the md-nve task
Keyword Description
steps The number of steps to consider for the simulation.

Keyword steps

steps = integers

The steps keyword specifies the number of MD steps to perform.

Default
Not any, this keyword must be specified.