### Typical CommandLineParser Usage

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1CommandLineParser.xhtml

Demonstrates the basic setup and usage of the CommandLineParser. Ensure to include the necessary header and handle potential errors.

```cpp
#include <gromacs/commandline/cmdlineparser.h>

gmx::Options options("name", "description");
// Fill up options
gmx::CommandLineParser(&options).parse(&argc, argv);
options.finish();
```

--------------------------------

### Notify Callbacks During Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/page_mdmodules.xhtml

During setup, for example within Mdrunner, you can trigger notifications by calling the appropriate callback function with the required argument. This example demonstrates how to notify a callback.

```C++
YourCallbackSignature argument(); mdModules_.notifier().notifier_.notify(argument); 
```

--------------------------------

### Get Domain Decomposition Grid Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/domdec__setup_8cpp.xhtml

Determines the DD grid setup.

```APIDOC
## getDDGridSetup

### Description
Determines the DD grid setup.

### Method
DDGridSetup

### Parameters
- **mdlog** (const gmx::MDLogger &) - MD logger object.
- **ddRole** (DDRole) - DD role.
- **mpiComm** (const gmx::MpiComm &) - MPI communicator.
- **numRanksRequested** (const int) - Number of ranks requested.
- **options** (const DomdecOptions &) - Domain decomposition options.
- **ddSettings** (const DDSettings &) - DD settings.
- **systemInfo** (const DDSystemInfo &) - System information.
- **cellSizeLimit** (const real) - Cell size limit.
- **mtop** (const gmx_mtop_t &) - Topology information.
- **ir** (const t_inputrec &) - Input record.
- **separatePmeRanksPermitted** (const gmx::SeparatePmeRanksPermitted &) - Permitted separate PME ranks.
- **box** (const matrix) - Simulation box dimensions.
- **xGlobal** (gmx::ArrayRef< const gmx::RVec >) - Global coordinates.
- **ddbox** (gmx_ddbox_t *) - Output domain decomposition box information.
```

--------------------------------

### File: bench_setup.h

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/dir_6cc3f6633093836886a4ce2735dc640b.xhtml

Declares functions for setting up kernel benchmarks.

```APIDOC
## File: bench_setup.h

### Description
This file declares functions for setting up kernel benchmarks.

### Method
N/A

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
N/A
```

--------------------------------

### Get Library File Finder

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/futil_8h.xhtml

Gets a finder object used for locating data files within the GROMACS installation's share/top/ directory.

```cpp
#include <gromacs/utility/filefinder.h>

const DataFileFinder & gmx::getLibraryFileFinder ();
```

--------------------------------

### Function Documentation: setupGpuDevicePeerAccess

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/gpu__utils_8h.xhtml

Documentation for the setupGpuDevicePeerAccess function.

```APIDOC
## Function Documentation
### void setupGpuDevicePeerAccess (gmx::ArrayRef< const int > gpuIdsToUse, const gmx::MDLogger &mdlog)
Enable peer access between GPUs where supported.

### Parameters
- **gpuIdsToUse** (gmx::ArrayRef< const int >) - Required - List of GPU IDs in use
- **mdlog** (const gmx::MDLogger &) - Required - Logger object
```

--------------------------------

### File: bench_setup.cpp

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/dir_6cc3f6633093836886a4ce2735dc640b.xhtml

Defines functions for setting up kernel benchmarks.

```APIDOC
## File: bench_setup.cpp

### Description
This file defines functions for setting up kernel benchmarks.

### Method
N/A

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
N/A
```

--------------------------------

### Template C++ Example

Source: https://manual.gromacs.org/2026.1/doxygen/html-user/examples.xhtml

A basic C++ template file for Gromacs examples. This serves as a starting point for developing new simulation scripts or analysis tools.

```cpp
#include <iostream>

int main() {
    std::cout << "Hello, Gromacs!\n";
    return 0;
}

```

--------------------------------

### Get CMake Installation Stages

Source: https://manual.gromacs.org/2026.1/dev-manual/gitlab-ci.html

Retrieves the stages necessary for requested CMake versions. An intermediate build stage is created for each CMake version, installed into '/usr/local/cmake-{version}'.

```python
scripted_gmx_docker_builds.get_cmake_stages(_*_ , _input_args : Namespace_, _base : str_)
```

--------------------------------

### Set up Python virtual environment

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Creates a virtual environment and installs essential build tools and MPI support.

```bash
python3 -m venv $HOME/myvenv
. $HOME/myvenv/bin/activate
python -m ensurepip --default-pip
pip install --upgrade pip setuptools wheel
pip install mpi4py
```

--------------------------------

### Setup Simple Simulation with gmxapi

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/usage.html

Use gmxapi.read_tpr to load simulation input and gmxapi.mdrun to set up the simulation. Execution is not triggered immediately.

```python
import gmxapi as gmx
simulation_input = gmx.read_tpr(tpr_filename)
md = gmx.mdrun(simulation_input)
```

--------------------------------

### Get Number of Grids

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/namespacegmx.xhtml

Returns the number of search grids based on the domain setup.

```cpp
static int | numGrids (const GridSet::DomainSetup &domainSetup)
```

--------------------------------

### void prepareTest(const char *filename)

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1test_1_1SetPrecisionUnSupportedFiles.xhtml

Sets up the test case before running by specifying the output file name.

```APIDOC
## void prepareTest(const char *filename)

### Description
Sets up the test case before running. This method is used to specify the output file name to determine the file type for the test.

### Parameters
#### Path Parameters
- **filename** (const char *) - Required - Name of the output file used to specify file type.
```

--------------------------------

### Get GROMACS configuration

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/pythonreference.html

Retrieves a read-only dictionary proxy containing information about the GROMACS installation used to configure the package.

```python
gmxapi.utility.config()
```

--------------------------------

### gmx::H5md::setupFromExistingFile

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/classgmx_1_1H5md-members.xhtml

Sets up the H5md object to read from an existing file.

```APIDOC
## setupFromExistingFile

### Description
Sets up the H5md object to read from an existing file.

### Method
void setupFromExistingFile()
```

--------------------------------

### Get DD Grid Setup Cell Size Limit

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/domdec__setup_8cpp.xhtml

Returns the minimum cell size (in nm) required for DD.

```APIDOC
## getDDGridSetupCellSizeLimit

### Description
Return the minimum cell size (in nm) required for DD.

### Method
real

### Parameters
- **mdlog** (const gmx::MDLogger &) - MD logger object.
- **bDynLoadBal** (const bool) - Dynamic load balancing flag.
- **dlb_scale** (const real) - Dynamic load balancing scale.
- **ir** (const t_inputrec &) - Input record.
- **systemInfoCellSizeLimit** (real) - System info cell size limit.
- **numRanksRequested** (int) - Number of ranks requested.
```

--------------------------------

### Implement main() using runAsMainCMain

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1CommandLineModuleManager.xhtml

Demonstrates how to wrap a custom main function using runAsMainCMain to handle common command-line options and startup tasks.

```cpp
int my_main(int argc, char *argv[])
{
// <...>
}
int main(int argc, char *argv[])
{
return gmx::CommandLineModuleManager::runAsMainCMain(argc, argv, &my_main);
}
```

--------------------------------

### Get Number of Search Grids

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/gridset_8cpp.xhtml

Returns the number of search grids based on the provided domain setup. This function is part of the GridSet utility.

```c++
static int | gmx::numGrids (const GridSet::DomainSetup &domainSetup)
```

--------------------------------

### void initSettingsNoNice

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/namespaceanonymous__namespace_02mdrun__main_8cpp_03.xhtml

Initializes a command line module with a default nice level of zero.

```APIDOC
## void initSettingsNoNice(gmx::CommandLineModuleSettings *settings)

### Description
Initializes a module that defaults to nice level zero.

### Parameters
#### Request Body
- **settings** (gmx::CommandLineModuleSettings*) - Required - Pointer to the command line module settings object.
```

--------------------------------

### Get Torch Support Description

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/applied__forces_2nnpot_2binary__information_8h.xhtml

Call this function to retrieve a string describing the Torch support in the currently running binary. No specific setup or imports are required beyond standard C++.

```cpp
std::string gmx::torchDescription ()
```

--------------------------------

### Implement OptionsVisitor for Iterating Options

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1OptionsIterator.xhtml

Implement the gmx::OptionsVisitor interface to iterate through sections and options within a Gromacs Options object. This example shows how to recursively visit all sections and options starting from a given section.

```cpp
#include <gromacs/options/optionsvisitor.h>

class Visitor : public gmx::OptionsVisitor
{
public:
virtual void visitSection(const OptionSectionInfo &section)
{
OptionsIterator iterator(section);
iterator.acceptSections(this);
iterator.acceptOptions(this);
}
virtual void visitOption(const OptionInfo &option)
{
// Do something.
}
}

Visitor().visitSection(options.rootSection());

```

--------------------------------

### Typical CommandLineModuleManager Usage

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1CommandLineModuleManager.xhtml

Demonstrates the standard setup and execution flow for the CommandLineModuleManager. Ensure all necessary modules are registered before calling run.

```cpp
#include <gromacs/commandline/cmdlinemodulemanager.h>
int main(int argc, char *argv[])
{
gmx::CommandLineProgramContext &programContext = gmx::initForCommandLine(&argc, &argv);
try
{
gmx::CommandLineModuleManager manager("gmx", &programContext);
// <register all necessary modules>
int rc = manager.run(argc, argv);
gmx::finalizeForCommandLine();
return rc;
}
catch (const std::exception &ex)
{
gmx::printFatalErrorMessage(stderr, ex);
return gmx::processExceptionAtExitForCommandLine(ex);
}
}
```

--------------------------------

### Specify GROMACS installation path

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Use the gmxapi_ROOT environment variable to point the installer to a valid GROMACS installation directory.

```bash
gmxapi_ROOT=/Users/eric/gromacs pip install --verbose gmxapi
```

--------------------------------

### Set Help Text Example

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml

Demonstrates how to define a string array and pass it to the setHelpText method.

```cpp
const char *const desc[] = {
"This is the description",
"for the options"
};
settings->setHelpText(desc);
```

--------------------------------

### Setup H5MD File from Input

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/namespacegmx.xhtml

Configures an H5MD file using topology and input record data. Requires an H5MD file handle, topology, and input record.

```cpp
void | setupFileFromInput (H5md *h5md, const gmx_mtop_t &topology, const t_inputrec &inputRecord)
```

--------------------------------

### Install gmxapi via environment variable

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Use the gmxapi_ROOT environment variable to specify the GROMACS installation path during pip installation.

```bash
gmxapi_ROOT=/path/to/gromacs pip install --no-cache-dir gmxapi
```

--------------------------------

### Install mpi4py

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Install mpi4py using the system MPI compiler.

```bash
MPICC=`which mpicc` pip install --no-cache-dir --upgrade mpi4py
```

--------------------------------

### ListedForces::setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classListedForces.xhtml

Sets up the listed interactions and thread parallelization. It copies interaction definitions and configures parameters based on input.

```APIDOC
## void ListedForces::setup

### Description
Copy the listed interactions from `idef` and set up the thread parallelization.

### Method
void

### Endpoint
N/A (Member function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (void)
This function does not return a value.

#### Response Example
None
```

--------------------------------

### Install Build Dependencies

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Install cmake and pybind11 required for building gmxapi.

```bash
pip install --upgrade cmake pybind11
```

--------------------------------

### setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-user/classgmx_1_1HaloExchange.xhtml

Sets up the halo communication. This method should be called after any (re)partitioning of the simulation domain.

```APIDOC
## void setup(gmx_domdec_t *dd, t_state *localState, const gmx_ddbox_t &ddbox, t_forcerec *fr, bool cellsChanged)

### Description
Sets up the halo communication. This method should be called after any (re)partitioning of the simulation domain.

### Parameters
#### Path Parameters
- **dd** (gmx_domdec_t *) - Pointer to the domain decomposition structure.
- **localState** (t_state *) - Pointer to the local state of the simulation.
- **ddbox** (const gmx_ddbox_t &) - The domain decomposition box information.
- **fr** (t_forcerec *) - Pointer to the force record.
- **cellsChanged** (bool) - Indicates if the simulation cells have changed.
```

--------------------------------

### Verify GROMACS installation

Source: https://manual.gromacs.org/2026.1/user-guide/getting-started.html

Check the installed version of GROMACS or troubleshoot command availability.

```bash
gmx -version
```

```bash
gmx: command not found.
```

--------------------------------

### Force Output Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-user/namespacegmx.xhtml

Initializes force buffers and handles clearing operations.

```C
static ForceOutputs setupForceOutputs (ForceHelperBuffers *forceHelperBuffers, ArrayRefWithPadding< RVec > force, const DomainLifetimeWorkload &domainWork, const StepWorkload &stepWork, const bool havePpDomainDecomposition, gmx_wallcycle *wcycle)
```

--------------------------------

### Install gmxapi package

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Sources the GROMACS environment script and installs the gmxapi package.

```bash
. /path/to/gromacs/bin/GMXRC
pip install --no-cache-dir gmxapi
```

--------------------------------

### void writeHelp(const HelpWriterContext &context)

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1anonymous__namespace_02selhelp_8cpp_03_1_1KeywordsHelpTopic.xhtml

Prints the help text for the selection keywords topic to the provided context.

```APIDOC
## void writeHelp(const HelpWriterContext &context)

### Description
Prints the help text for the KeywordsHelpTopic to the specified HelpWriterContext.

### Parameters
#### Path Parameters
- **context** (HelpWriterContext) - Required - The context object used for writing the help output.

### Exceptions
- **std::bad_alloc** - Thrown if the system is out of memory.
- **FileIOError** - Thrown on any I/O error during the writing process.
```

--------------------------------

### Installation Path Discovery

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/group__module__commandline.xhtml

Functions for finding GROMACS installation paths and related information.

```APIDOC
## gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::isAcceptableLibraryPath

### Description
Returns whether a given path contains files from `share/top/`.

### Method
N/A (Function)

### Endpoint
N/A

### Parameters
- **path** (const std::filesystem::path&) - Input - The path to check.

### Response
bool - True if the path is acceptable, false otherwise.
```

```APIDOC
## gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::isAcceptableLibraryPathPrefix

### Description
Returns whether a given path prefix contains files from `share/top/`.

### Method
N/A (Function)

### Endpoint
N/A

### Parameters
- **path** (const std::filesystem::path&) - Input - The path prefix to check.

### Response
bool - True if the path prefix is acceptable, false otherwise.
```

```APIDOC
## gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::findFallbackInstallationPrefixPath

### Description
Returns a fallback installation prefix path.

### Method
N/A (Function)

### Endpoint
N/A

### Parameters
None

### Response
std::filesystem::path - The fallback installation prefix path.
```

```APIDOC
## gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::findInstallationPrefixPath

### Description
Generic function to find data files based on the path of the binary.

### Method
N/A (Function)

### Endpoint
N/A

### Parameters
- **binaryPath** (const std::filesystem::path&) - Input - The path to the binary.
- **bSourceLayout** (bool*) - Output - Pointer to a boolean indicating if it's a source layout.

### Response
std::filesystem::path - The installation prefix path.
```

--------------------------------

### gmx::H5md::setupFileFromInput

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/classgmx_1_1H5md.xhtml

Sets up the HDF5 file using provided topology and input record data.

```APIDOC
## POST /h5md/setupFileFromInput

### Description
Set up the file from input data.

### Method
POST

### Endpoint
/h5md/setupFileFromInput

### Parameters
#### Request Body
- **topology** (const gmx_mtop_t &) - Required - Topology data of system.
- **inputRecord** (const t_inputrec &) - Required - Simulation parameters.

### Request Example
```json
{
  "topology": {},
  "inputRecord": {}
}
```

### Response
#### Success Response (200)
- **status** (string) - Indicates the success of the setup operation.

#### Response Example
```json
{
  "status": "success"
}
```
```

--------------------------------

### frameStarted

Source: https://manual.gromacs.org/2026.1/doxygen/html-user/classgmx_1_1AnalysisDataModuleSerial.xhtml

Called at the start of each data frame. Receives header information for the frame that is starting.

```APIDOC
## void gmx::AnalysisDataModuleSerial::frameStarted(const AnalysisDataFrameHeader & _frame_)

### Description
Called at the start of each data frame. Receives header information for the frame that is starting.

### Method
void

### Parameters
- **_frame_** (const AnalysisDataFrameHeader &) - Required - Header information for the frame that is starting.

### Exceptions
- unspecified: Can throw any exception required by the implementing class to report errors.
```

--------------------------------

### start

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1internal_1_1OptionSectionImpl.xhtml

Called when entering the section. It calls AbstractOptionStorage::startSource() for all options.

```APIDOC
## start

### Description
Called when entering the section. Calls AbstractOptionStorage::startSource() for all options.

### Method
`void gmx::internal::OptionSectionImpl::start()`

### Endpoint
N/A (Member function)

### Parameters
None

### Request Example
N/A

### Response
None (void function).
```

--------------------------------

### Function: isTransformationPullSetup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/namespacegmx_1_1test_1_1anonymous__namespace_02pull_8cpp_03.xhtml

Checks if a given pull setup name corresponds to a transformation pull setup.

```APIDOC
## Function: isTransformationPullSetup

### Description
Determines if the provided pull setup name is a transformation pull setup.

### Parameters
- **pullSetupName** (const std::string &) - Required - The name of the pull setup to check.

### Response
- **bool** - Returns true if the setup is a transformation pull setup, false otherwise.
```

--------------------------------

### Setup Force Outputs

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/namespacegmx.xhtml

Sets up different force buffers and performs clearing. This is essential for managing force data during simulations.

```cpp
static ForceOutputs | setupForceOutputs (ForceHelperBuffers *forceHelperBuffers, ArrayRefWithPadding< RVec > force, const DomainLifetimeWorkload &domainWork, const StepWorkload &stepWork, const bool havePpDomainDecomposition, gmx_wallcycle *wcycle)
```

--------------------------------

### HelpWriterContext::writeOptionListStart

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1HelpWriterContext.xhtml

Starts writing a list of options.

```APIDOC
## void gmx::HelpWriterContext::writeOptionListStart() const

### Description
Starts writing a list of options. Prints any necessary headers for a list of options formatted with writeOptionItem().

### Method
void

### Endpoint
N/A (Member Function)

### Parameters
N/A

### Request Example
N/A

### Response
#### Success Response (void)
N/A

#### Response Example
N/A

### Exceptions
N/A
```

--------------------------------

### Domain Decomposition Grid Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/domdec__setup_8cpp.xhtml

Function to determine the Domain Decomposition (DD) grid setup.

```APIDOC
## getDDGridSetup

### Description
Determines the DD grid setup. Either implements settings required by the user, or otherwise chooses estimated optimal number of separate PME ranks and DD grid cell setup, DD cell size limits, and the initial ddbox.

### Method
(Implicitly a setup function, likely internal)

### Endpoint
N/A (Internal function)

### Parameters
- **_mdlog_** (const gmx::MDLogger &) - Description not specified
- **_ddRole_** (DDRole) - Description not specified
- **_mpiComm_** (const gmx::MpiComm &) - Description not specified
- **_numRanksRequested_** (int) - Description not specified
- **_options_** (const gmx::DomdecOptions &) - Description not specified
- **_ddSettings_** (const DDSettings &) - Description not specified
- **_systemInfo_** (const DDSystemInfo &) - Description not specified
- **_cellSizeLimit_** (real) - Description not specified
- **_mtop_** (const gmx_mtop_t &) - Description not specified
- **_ir_** (const t_inputrec &) - Description not specified
- **_separatePmeRanksPermitted_** (const gmx::SeparatePmeRanksPermitted &) - Description not specified
- **_box_** (const matrix) - Description not specified
- **_xGlobal_** (gmx::ArrayRef< const gmx::RVec >) - Description not specified
- **_ddbox_** (gmx_ddbox_t *) - Description not specified

### Response
#### Success Response (DDGridSetup)
- **Return Value** (DDGridSetup) - The determined DD grid setup.

### Response Example
(No example provided)
```

--------------------------------

### Include Headers for Benchmark System Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/bench__system_8h.xhtml

Includes necessary headers for setting up a benchmark system in C++. Ensure these headers are available in your project.

```cpp
#include <cstdint>
#include <cstdio>
#include <string>
#include <vector>
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vectypes.h"
```

--------------------------------

### Install gmxapi from GROMACS source

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Build and install the gmxapi package directly from the GROMACS source repository.

```bash
cd python_packaging/gmxapi
pip install -r requirements.txt
pip install .
```

--------------------------------

### gmx::H5md::setupFromExistingFile

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/classgmx_1_1H5md.xhtml

Sets up the HDF5 file by scanning for existing trajectory data, primarily in the /particles/system group.

```APIDOC
## POST /h5md/setupFromExistingFile

### Description
Set up from an existing file. Scans for trajectory data available in the /particles/system group of the HDF5 file. For trajectories written by GROMACS this group contains data for all atoms in the simulated system.

### Method
POST

### Endpoint
/h5md/setupFromExistingFile

### Note
Ignores trajectory data in other subgroups of /particles.

### Response
#### Success Response (200)
- **status** (string) - Indicates the success of the setup operation.

#### Response Example
```json
{
  "status": "success"
}
```
```

--------------------------------

### VelocityScalingTemperatureCoupling Setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1VelocityScalingTemperatureCoupling.xhtml

Performs sanity checks at setup time for the VelocityScalingTemperatureCoupling element. This is an override of the ISimulatorElement interface.

```c++
void elementSetup () override
```

--------------------------------

### Install gmxapi

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Commands to install the latest gmxapi release, including options for source distribution and pre-release versions.

```bash
# Get the latest official release.
pip install --no-cache-dir gmxapi
```

```bash
pip download gmxapi
pip install gmxapi-<version>.tar.gz
```

```bash
# Get the latest version, including pre-release versions.
pip install --no-cache-dir --pre gmxapi
```

--------------------------------

### ListedForces Setup Function

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classListedForces.xhtml

Copies listed interactions and sets up thread parallelization. Requires interaction definitions, number of atoms, GPU usage flag, and restraint indices.

```cpp
void | setup (const InteractionDefinitions &domainIdef, int numAtomsForce, bool useGpu, gmx::ArrayRef< const unsigned short > restraintComIndices)
```

--------------------------------

### Install pybind11 dependency

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Install the pybind11 package manually if the build process fails due to missing build-time dependencies.

```bash
pip install --upgrade pybind11
```

--------------------------------

### Setup H5md File from Input

Source: https://manual.gromacs.org/2026.1/doxygen/html-user/namespacegmx.xhtml

Sets up an H5md file from topology and input record data. Used for initializing trajectory files.

```cpp
setupFileFromInput (H5md *h5md, const gmx_mtop_t &topology, const t_inputrec &inputRecord)
```

--------------------------------

### POST /gmx/writeCommandLineHelpCMain

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/group__module__commandline.xhtml

Helper to implement help documentation for C-like main functions.

```APIDOC
## POST /gmx/writeCommandLineHelpCMain

### Description
Helper to implement ICommandLineModule::writeHelp() with a C-like main() function.

### Parameters
#### Request Body
- **context** (const CommandLineHelpContext &) - Required - Context object for writing help.
- **name** (const char *) - Required - Name of the module.
- **mainFunction** (int(*)(int argc, char *argv[])) - Required - C-like main function pointer.
```

--------------------------------

### Build and install gmxapi offline

Source: https://manual.gromacs.org/2026.1/gmxapi/userguide/install.html

Download wheels or source distributions with dependencies to a directory for later installation in an offline environment.

```bash
# Remove any locally cached (previously built) wheels.
pip cache remove gmxapi

# Download gmxapi and dependencies from pypi.
pip wheel --wheel-dir DIR gmxapi
# or, using package source from the GROMACS repository
cd python_packaging/gmxapi
pip wheel --wheel-dir DIR .

# Later, install.
pip install --no-index --find-links=DIR DIR/gmxapi*whl
```

```bash
# if in the GROMACS source repository
cd python_packaging/gmxapi
# or download and expand the archive
pip download --destination-directory DIR gmxapi
tar xf DIR/gmxapi*
cd gmxapi*

# Pre-fetch dependencies to DIR
pip download --destination-directory DIR .

# Build and install from the source directory.
pip install --no-index --find-links=DIR .
```

--------------------------------

### Method: startSet

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1AbstractOptionStorage.xhtml

Documentation for the startSet method which manages the transition between option value sources.

```APIDOC
## startSet

### Description
Starts adding values from a new source for the option. This marks the current value of the option as a default value, causing the next call to startSet() to clear it, allowing values from the new source to overwrite old values.

### Exceptions
This method does not throw.
```

--------------------------------

### gmx_fft_destroy

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/fft_8h.xhtml

Releases an FFT setup structure and all allocated memory. This function should be called after all transforms using a specific setup have been completed.

```APIDOC
## gmx_fft_destroy

### Description
Release an FFT setup structure.
Destroy setup and release all allocated memory.

### Method
void

### Endpoint
gmx_fft_destroy(gmx_fft_t _setup_)

### Parameters
#### Path Parameters
- **setup** (gmx_fft_t) - Setup returned from gmx_fft_init_1d(), or one of the other initializers.
```

--------------------------------

### void gmx::init(int *argc, char ***argv)

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/init_8cpp.xhtml

Initializes the GROMACS library environment.

```APIDOC
## void gmx::init(int *argc, char ***argv)

### Description
Initializes the GROMACS library. This function should be called at the start of the application.

### Parameters
#### Path Parameters
- **argc** (int*) - Required - Pointer to the number of command-line arguments.
- **argv** (char***) - Required - Pointer to the array of command-line argument strings.
```

--------------------------------

### gmx::MDModules::subscribeToSimulationSetupNotifications

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1MDModules.xhtml

Subscribes MDModules to simulation setup notifications, allowing callbacks during the setup phase after options are assigned.

```APIDOC
## void gmx::MDModules::subscribeToSimulationSetupNotifications

### Description
Subscribe MDModules to simulation setup notifications. Allows MDModules to subscribe to notifications that are called back during the set up of an MD simulation, after the options were assigned to the modules.

### Method
void

### Endpoint
N/A (Member function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None
```

--------------------------------

### gmx::HaloExchange::setup

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/classgmx_1_1HaloExchange-members.xhtml

Sets up the halo exchange mechanism.

```APIDOC
## gmx::HaloExchange::setup

### Description
Sets up the halo exchange mechanism for parallel simulations. This method configures the exchange based on domain decomposition and simulation state.

### Method
(Not specified, likely a member function call)

### Parameters
* **dd** (gmx_domdec_t *) - Pointer to the domain decomposition structure.
* **localState** (t_state *) - Pointer to the local simulation state.
* **ddbox** (const gmx_ddbox_t &) - The domain decomposition box information.
* **fr** (t_forcerec *) - Pointer to the force record.
* **cellsChanged** (bool) - Flag indicating if the simulation cells have changed.
```

--------------------------------

### Start Frames Analysis

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/group__module__trajectoryanalysis.xhtml

Starts the analysis of frames for various trajectory analysis modules. This function is necessary for threaded parallelization.

```APIDOC
## TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance::startFrames

### Description
Starts the analysis of frames.

### Method
override virtual

### Parameters
- **opt** (const AnalysisDataParallelOptions &) - in - Parallel options
- **selections** (const SelectionCollection &) - in - Frame-local selection collection object.

### Returns
Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

### See Also
- TrajectoryAnalysisModuleData
Reimplemented from gmx::TrajectoryAnalysisModule.
```

```APIDOC
## TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf::startFrames

### Description
Starts the analysis of frames.

### Method
override virtual

### Parameters
- **opt** (const AnalysisDataParallelOptions &) - in - Parallel options
- **selections** (const SelectionCollection &) - in - Frame-local selection collection object.

### Returns
Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

### See Also
- TrajectoryAnalysisModuleData
Reimplemented from gmx::TrajectoryAnalysisModule.
```

```APIDOC
## TrajectoryAnalysisModuleDataPointer gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa::startFrames

### Description
Starts the analysis of frames.

### Method
override virtual

### Parameters
- **opt** (const AnalysisDataParallelOptions &) - in - Parallel options
- **selections** (const SelectionCollection &) - in - Frame-local selection collection object.

### Returns
Data structure for thread-local data.

This function is necessary only for threaded parallelization. It is called once for each thread and should initialize a class that contains any required frame-local data in the returned value. The default implementation creates a basic data structure that holds thread-local data handles for all data objects registered with registerAnalysisDataset(), as well as the thread-local selection collection. These can be accessed in analyzeFrame() using the methods in TrajectoryAnalysisModuleData. If other thread-local data is needed, this function should be overridden and it should create an instance of a class derived from TrajectoryAnalysisModuleData.

### See Also
- TrajectoryAnalysisModuleData
Reimplemented from gmx::TrajectoryAnalysisModule.
```

--------------------------------

### gmx::H5md::setupFromExistingFileForAppending

Source: https://manual.gromacs.org/2026.1/doxygen/html-lib/classgmx_1_1H5md-members.xhtml

Sets up the H5md object for appending data to an existing file.

```APIDOC
## setupFromExistingFileForAppending

### Description
Sets up the H5md object for appending data to an existing file.

### Method
void setupFromExistingFileForAppending(int64_t restartingFromStep, int64_t numParticles)

### Parameters
#### Path Parameters
- **restartingFromStep** (int64_t) - Required - The step number to restart from.
- **numParticles** (int64_t) - Required - The number of particles in the system.
```

--------------------------------

### Start GPU Profiler (CUDA)

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/gpu__utils__hip_8cpp.xhtml

Starts the GPU profiler for CUDA when mdrun is being profiled. This is controlled by the NVPROF_ID environment variable.

```cpp
void startGpuProfiler ()

```

--------------------------------

### Gro File Format Example

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/programs_2mdrun_2tests_2pull__rotation_8cpp.xhtml

Example of a .gro file format for atomic positions, used in mdrun rotation tests.

```gro
4
1AR      AR    1   1.500   1.500   3.200
2AR      AR    2   3.900   5.800   3.500
3AR      AR    3   4.700   6.200   2.100
4AR      AR    4   5.500   4.000   6.600
8.000 8.000 8.000


```

--------------------------------

### QMMMSimulationParameterSetup Class Methods

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMSimulationParameterSetup.xhtml

Methods for configuring and retrieving QM/MM simulation parameters.

```APIDOC
## QMMMSimulationParameterSetup Methods

### Description
Provides methods to set and retrieve configuration parameters for QM/MM simulations, such as local atom sets, logger instances, and MPI communicators.

### Methods
- **setLocalQMAtomSet(const LocalAtomSet &localAtomSet)**: Sets the local atom set for QM atoms.
- **setLocalMMAtomSet(const LocalAtomSet &localAtomSet)**: Sets the local atom set for MM atoms.
- **localQMAtomSet()**: Returns the local atom set for QM atoms. Throws InternalError if not set.
- **localMMAtomSet()**: Returns the local atom set for MM atoms. Throws InternalError if not set.
- **setPeriodicBoundaryConditionType(const PbcType &pbc)**: Sets the periodic boundary condition.
- **periodicBoundaryConditionType()**: Returns the current periodic boundary condition type.
- **setLogger(const MDLogger &logger)**: Sets the logger for QMMM during mdrun.
- **logger()**: Returns the current logger instance.
- **setMpiComm(const MpiComm &mpiComm)**: Sets the MPI communicator for QMMM during mdrun startup.
- **mpiComm()**: Returns the current MPI communicator.
```

--------------------------------

### Simulation Setup Notifier

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/structgmx_1_1MDModulesNotifiers.xhtml

Handles subscribing and calling callbacks during simulation setup. It provides modules with various simulation parameters and data.

```APIDOC
## SimulationSetupNotifier

### Description
Handles subscribing and calling callbacks during simulation setup. Provides modules with the internal data they wrote to .tpr files, allows adding atom indices to local atom sets, provides starting behavior, logging class, topology, enables reporting energy output preferences, disabling PME ranks, provides PBC type, time-step, ensemble temperature, communicator, multisim data, plain pairlist ranges, input filenames, direct provider, and Plumed input filename.

### Template Parameters
- **KeyValueTreeObject&** (type) - Provides modules with the internal data they wrote to .tpr files.
- **LocalAtomSetManager*** (type) - Enables modules to add atom indices to local atom sets to be managed.
- **StartingBehavior&** (type) - Provides modules with the starting behavior of the simulation.
- **MDLogger&** (type) - Allows MdModule to use standard logging class for messages output.
- **gmx_mtop_t&** (type) - Provides the topology of the system to the modules.
- **MDModulesEnergyOutputToDensityFittingRequestChecker*** (type) - Enables modules to report if they want to write their energy output to the density fitting field in the energy files.
- **MDModulesEnergyOutputToQMMMRequestChecker*** (type) - Enables QMMM module to report if it wants to write its energy output to the "Quantum En." field in the energy files.
- **MDModulesEnergyOutputToNNPotRequestChecker*** (type) - Enables NNPot module to report if it wants to write its energy output to the "NN Potential" field in the energy files.
- **SeparatePmeRanksPermitted*** (type) - Enables modules to report if they want to disable dedicated PME ranks.
- **PbcType&** (type) - Provides modules with the periodic boundary condition type that is used during the simulation.
- **SimulationTimeStep&** (type) - Provides modules with the simulation time-step that allows them to interconvert between step and time information.
- **EnsembleTemperature&** (type) - Provides modules with the (eventual) constant ensemble temperature.
- **MpiComm&** (type) - Provides a communicator to the modules during simulation setup.
- **gmx_multisim_t*** (type) - Provides access to multisim data.
- **PlainPairlistRanges*** (type) - Provides access to plain pairlist ranges.
- **MdRunInputFilename** (type) - Provides the input filename for the MD run.
- **EdrOutputFilename** (type) - Provides the output filename for the EDR file.
- **MDModulesDirectProvider*** (type) - Provides direct access to simulation data.
- **PlumedInputFilename** (type) - Provides the Plumed input filename.
```

--------------------------------

### Constructor: gmx::BenchmarkSystem

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/structgmx_1_1BenchmarkSystem.xhtml

Initializes a new benchmark system by stacking cubic boxes of water molecules.

```APIDOC
## Constructor gmx::BenchmarkSystem

### Description
Generates a benchmark system of size multiplicationFactor times the base size by stacking cubic boxes of 1000 water molecules with 3000 atoms total.

### Parameters
#### Path Parameters
- **multiplicationFactor** (int) - Required - Should be a power of 2, is checked.
- **outputFile** (const std::string &) - Required - The name of the csv file to write benchmark results.
```

--------------------------------

### Notify Start of Each Data Frame

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1AnalysisDataSimpleHistogramModule.xhtml

Callback function called at the start of each data frame. It receives header information for the current frame.

```cpp
void frameStarted(const AnalysisDataFrameHeader &header) override
```

--------------------------------

### setupMTop Function

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/namespacegmx_1_1test_1_1anonymous__namespace_02massrepartitioning_8cpp_03.xhtml

Documentation for the setupMTop function within the Gromacs library.

```APIDOC
## void setupMTop (gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds)

### Description
Initializes the molecular topology structure (mtop) using provided masses and bond information.

### Method
N/A (Function Signature)

### Endpoint
N/A (Internal Function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (void)
This function does not return a value; it modifies the `mtop` structure in place.

#### Response Example
None
```

--------------------------------

### AnalysisDataHandle::startFrame

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1AnalysisDataHandle.xhtml

Starts data recording for a new frame, optionally including an x-value and its error. Each frame index should be started exactly once.

```APIDOC
## void gmx::AnalysisDataHandle::startFrame(size_t _index_, real _x_, real _dx_ = `0.0`)

### Description
Start data for a new frame.

### Method
void

### Endpoint
N/A (Member Function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **index** (size_t) - Required - Zero-based index for the frame to start.
- **x** (real) - Required - x value for the frame.
- **dx** (real) - Optional - Error in x for the frame if applicable. Defaults to `0.0`.

### Request Example
```json
{
  "index": 0,
  "x": 10.5,
  "dx": 0.1
}
```

### Response
#### Success Response
None

#### Response Example
```
// No direct response body for this function
```

### Exceptions
- **unspecified**: Any exception thrown by attached data modules in IAnalysisDataModule::frameStarted().
```

--------------------------------

### Run Single Module with Custom Settings

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1CommandLineModuleManager.xhtml

Implements a main() method that runs a given function with custom settings. It additionally calls a settings function to initialize CommandLineModuleSettings, allowing for custom configurations like a different default nice level.

```cpp
int gmx::CommandLineModuleManager::runAsMainCMainWithSettings(int _argc_, char *_argv_[], CMainFunction _mainFunction_, InitSettingsFunction _settingsFunction_)
```

--------------------------------

### init

Source: https://manual.gromacs.org/2026.1/doxygen/html-full/classgmx_1_1CommandLineHelpModule.xhtml

Initializes the module and provides settings for the runner. This method is currently not called when writing the help.

```APIDOC
## void gmx::CommandLineHelpModule::init

### Description
Initializes the module and provides settings for the runner. This will be called before run(), and can be used to adjust initialization that the runner does. This method is currently not called when writing the help.

### Method
void

### Endpoint
N/A (Member Function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
None

#### Response Example
None

### Exceptions
None explicitly mentioned, but may throw exceptions as per ICommandLineModule implementation.
```