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_number ,
detect |
tis |
repptis |
A replica exchange partial path transition interface sampling simulation. | task , steps ,
interfaces |
tis |
pptis |
A partial path transition interface sampling simulation. | task , steps ,
interfaces |
tis |
explore |
A free energy surface exploration simulation. | task , steps ,
interfaces |
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 total retis steps (cycles) |
interfaces | The location of the interfaces to consider. |
priority_shooting | Prioritize the ensembles with less cycles. |
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.
Note that it indicates the goal/final number of the simulation cycles.
- 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.
Keyword priority_shooting¶
If True
, ensembles with lower cycle numbers will be prioritized
until their cycle numbers equals the others.
This setting simplify the use of PyRETIS in cluster environments in which walltime is rather short. Each ensemble can be, therefore, investigated also if launching several runs.
- Default
- The default value is
priority_shooting = False
.
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_number = 1
Keywords for the tis task¶
For the tis
task, the following keywords can be set:
Keyword | Description |
---|---|
steps | The total number of steps to perform. |
interfaces | The interfaces defining the TIS ensemble. |
priority_shooting | Prioritize the ensembles with less cycles. |
ensemble_number | For defining the ensemble number considered. |
detect | The interface used for detecting successful paths. |
maxlegth | The maximum number of step allowed for a 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 priority_shooting¶
If True
, ensembles with lower cycle numbers will be prioritized
until their cycle numbers equals the others.
This setting simplify the use of PyRETIS in cluster environments in which walltime is rather short. Each ensemble can be, therefore, investigated also if launching several runs.
- Default
- The default value is
priority_shooting = False
.
Keyword ensemble_number¶
A number specifying the path ensemble we are simulating,
ensemble_number = 1
corresponds to [0^+]
, 2 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 repptis task¶
The repptis
task defines a replica exchange partial path
transition interface sampling simulation. Paths between adjacent
pptis
ensembles can be swapped using the replica exchange move.
Simulation
----------
task = repptis
steps = 20000
interfaces = [-0.5, -0.3, 0, 0.3, 0.5]
Keywords for the repptis task¶
For the repptis
task, the following keywords can be set:
Keyword | Description |
---|---|
steps | The number of total repptis steps (cycles) |
interfaces | The location of the interfaces to consider. |
priority_shooting | Prioritize the ensembles with less cycles. |
In addition, this task requires that the sections TIS and RETIS are defined.
Note that (RE)PPTIS simulations make use of the TIS and RETIS sections in the input RST file. This is because almost all of the keywords are similar. Therefore, REPPTIS or PPTIS sections do not exist in the RST file, but re-use the TIS and RETIS sections.
Keyword steps¶
The steps
keyword defines the number of REPPTIS cycles to perform.
Note that it indicates the goal/final number of the simulation cycles.
- 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.
Keyword priority_shooting¶
If True
, ensembles with lower cycle numbers will be prioritized
until their cycle numbers equals the others.
This setting simplify the use of PyRETIS in cluster environments in which walltime is rather short. Each ensemble can be, therefore, investigated also if launching several runs.
- Default
- The default value is
priority_shooting = False
.
The pptis task¶
The pptis
task defines a partial path transition interface sampling
simulation. PPTIS ensembles are shorter than TIS ensembles, cutting the paths’
memory requirements. While for (RE)TIS the paths of [i^+]
need to start from state A
, cross interface i
, and either commit to
state B
or return to state A
, PPTIS paths of [i^+-]
only need to
start and end at interfaces i-1
or i+1
, having crossed interface i
.
Simulation
----------
task = pptis
steps = 20000
interfaces = [-0.5, -0.3, 0, 0.3, 0.5]
Keywords for the pptis task¶
For the pptis
task, the following keywords can be set:
Keyword | Description |
---|---|
steps | The total number of steps to perform. |
interfaces | The interfaces defining the PPTIS ensemble. |
priority_shooting | Prioritize the ensembles with less cycles. |
In addition, this task requires that the section TIS is defined.
Note that PPTIS
simulations use the TIS section, and not the PPTIS section (which does not exist!).
Keyword steps¶
The steps
keyword defines the number of PPTIS 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 PPTIS simulation will be performed, otherwise, input files
for several single PPTIS simulations will be written.
These simulations can then be run manually.
- Default
- Not any, this keyword must be specified.
Keyword priority_shooting¶
If True
, ensembles with lower cycle numbers will be prioritized
until their cycle numbers equals the others.
This setting simplify the use of PyRETIS in cluster environments in which walltime is rather short. Each ensemble can be, therefore, investigated also if launching several runs.
- Default
- The default value is
priority_shooting = False
.
The explore task¶
The explore
task is a molecular dynamics simulation for
exploring the free energy landscape of a transition. It uses
the TIS path simulation approach to allow the exploration
of different regions with different moves.
The idea is to generate paths in order to explore the region delimited
by the first and the last given interface. The generated trajectories
will always be accepted.
To generate more often new paths, with the keyword maxlegth,
present in tis
input section, it is possible to limitate the length
of the generated trajectory.
This is a simple strategy to try to locate local minima when exploring an unknown free energy landscape.
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 overall 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. |
startcycle | Specifies the cycle step the simulation should start at. |
remove_generate | Specifies if the generated files should be removed after every ensemble TIS move. |
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. To be used,
it requires that method
keyword in the initial-path
section
is set to restart
.
- Default
- The default value is
pyretis.restart
.
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
.
Keyword remove_generate¶
The remove_generate
keyword specifies whether the generated files should
be removed after every ensemble TIS move. This is useful when running TIS
simulations in a cluster environment, where the generated files can
take up a lot of space. If remove_generate = True
, the generated files
will be removed after every ensemble TIS move. If remove_generate = False
,
the generated files will only be removed after an entire cycle has finished.
- Default
- The default value is
True
.