The simulation section¶
The simulation
section defines and selects the simulation PyRETIS will run.
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. Further, a specific task might also require
additional sections to be defined
as detailed in the table below:
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 may require different keywords, these are described below individually. In addition, there are some settings which typically are used in relation to the analysis, or when extending simulations. These are described in the section on common keywords.
The retis task¶
The retis
task defines a replica exchange transition
interface sampling simulation.
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:
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¶
The steps
keyword defines the number of RETIS cycles to perform.
- Default
- Not any, this keyword must be specified.
Keyword interfaces¶
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.
Simulation
----------
task = tis
steps = 20000
interfaces = [-0.9, -0.8, -0.7, -0.6, -0.5, -0.4, -0.3, 1.0]
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:
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¶
The steps
keyword defines the number of TIS cycles to perform.
- Default
- Not any, this keyword must be specified.
Keyword interfaces¶
The interfaces
keyword specifies the interfaces to use in the
path simulation. If the number of interfaces given is 3 or less,
a single TIS simulation will be performed, 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¶
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¶
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.
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:
Keyword | Description |
---|---|
steps | Defines the number of steps to carry out. |
interfaces | Defines the interfaces to consider for the flux simulation. |
Keyword steps¶
The steps
keyword specifies the number of MD steps to perform.
- Default
- Not any, this keyword must be specified.
Keyword interfaces¶
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.
Simulation
----------
task = md-nve
steps = 10000000
Keywords for the md-nve task¶
The following keywords can be specified for the md-nve
task:
Keyword | Description |
---|---|
steps | The number of steps to consider for the simulation. |
Keyword steps¶
The steps
keyword specifies the number of MD steps to perform.
- Default
- Not any, this keyword must be specified.
Common keywords¶
The following keywords are common to all simulation tasks:
Keyword | Description |
---|---|
endcycle | Specifies the cycle step the simulation ended. |
exe-path | Specifies the directory from where the simulation was executed. |
restart | Specifies the restart file to use, and specifies that a restart should be done. |
startcycle | Specifies the cycle step the simulation should start at. |
Keyword endcycle¶
The endcycle
keyword specifies the cycle number at which the
simulation ended. If the simulation was stopped before the specified
number of steps were reached, the endcycle
will be difference
from the steps
keyword. This keyword will be set and updated
by PyRETIS and written to the processed input file.
- Default
- Not any, note that this keyword will be updated and modified by PyRETIS as part of the output process. This keyword is only used by the analysis program.
Keyword exe-path¶
The exe-path
keyword specifies the location from where the simulation
was executed. This will be set and updated by PyRETIS.
- Default
- Not any, note that this keyword will be updated and modified by PyRETIS as part of the output process. This keyword does not need to be set in the input file by the user since PyRETIS will update this setting automatically.
Keyword restart¶
The restart
keyword specifies the path to the restart file to use
for restarting/continuing the selected simulation task.
- Default
- Not any.
Keyword startcycle¶
The startcycle
keyword specifies the cycle number the simulation
starts at. This can be used, for instance, when extending a simulation
to tell PyRETIS that the simulation should start at a specified
step number.
- Default
- The default value is
0
.