### OPES Example Input Configuration

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Example configuration for OPES with adaptive kernel bandwidth, neighbor list, and PMF based on reweighting. This setup includes defining colvars, and configuring OPES metadynamics parameters.

```colvars
colvarsTrajFrequency			500
  
colvar {
 name phi
 lowerBoundary -180
 upperBoundary 180
 width 5.0
 dihedral {
 group1 {atomNumbers { 5 }}
 group2 {atomNumbers { 7 }}
 group3 {atomNumbers { 9 }}
 group4 {atomNumbers { 15}}
 }
}

colvar {
 name psi
 lowerBoundary -180
 upperBoundary 180
 width 5.0
 dihedral {
 group1 {atomNumbers { 7 }}
 group2 {atomNumbers { 9 }}
 group3 {atomNumbers { 15 }}
 group4 {atomNumbers { 17 }}
 }
}
  
opes_metad {
 colvars phi psi
 newHillFrequency 500
 barrier 11.950286806883364
 adaptiveSigma on
 neighborList on
 printTrajectoryFrequency 500
 pmf on
 pmfColvars phi psi
 pmfHistoryFrequency 1000
 outputEnergy on
}

```

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

### Example EBmetaD Configuration

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

A practical example demonstrating the configuration of EBmetaD for a single collective variable.

```APIDOC
## Example EBmetaD Configuration

### Description
This example shows how to configure Ensemble-Biased Metadynamics (EBmetaD) for a single collective variable named 'r', which is defined as the distance between two groups of atoms.

### Configuration:

```
colvar {
  name r
  distance {
    group1 { atomNumbers 991 992 }
    group2 { atomNumbers 1762 1763 }
  }
  upperBoundary  100.0
  width          0.1
}

metadynamics {
  name           ebmeta
  colvars        r
  hillWeight     0.01
  hillWidth      3.0
  ebMeta         on
  targetDistFile my_target_distribution.dat
  # Optional parameters for EBmetaD:
  # ebMetaEquilSteps 10000
  # targetDistMinVal 0.00001
}
```

### Explanation:

*   The `colvar` block defines a collective variable `r` based on the distance between specified atom groups.
*   The `metadynamics` block configures the metadynamics simulation:
    *   `name`: Assigns a name 'ebmeta' to this metadynamics instance.
    *   `colvars`: Links this metadynamics to the collective variable `r`.
    *   `hillWeight` and `hillWidth`: Standard metadynamics parameters.
    *   `ebMeta on`: Activates the Ensemble-Biased Metadynamics.
    *   `targetDistFile my_target_distribution.dat`: Specifies the file containing the target probability distribution.
    *   `ebMetaEquilSteps` (commented out): An optional parameter to set the number of equilibration steps.
    *   `targetDistMinVal` (commented out): An optional parameter to set the minimum value of the target distribution.
```

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

### MLCV Configuration Example

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

An example configuration for the NeuralNetwork colvar component, demonstrating how to set up a dense neural network with two hidden layers using external weight and bias files.

```APIDOC
## POST /colvars/configure

### Description
Configures the Dense Neural Network (MLCV) component within Colvars. This component calculates a non-linear combination of other scalar colvar components using a dense neural network.

### Method
POST

### Endpoint
/colvars/configure

### Parameters
#### Request Body
- **name** (string) - Required - The name of the colvar.
- **NeuralNetwork** (object) - Required - Configuration for the neural network.
  - **output_component** (integer) - Required - Specifies the output node to be used as the value of this CV (starting from 0).
  - **layer[i]_WeightsFile** (string) - Required - Path to the plain text file containing weights from layer i-1 to layer i. The index 'i' starts from 1.
  - **layer[i]_BiasesFile** (string) - Required - Path to the plain text file containing biases for layer i. The index 'i' starts from 1.
  - **layer[i]_activation** (string) - Optional - Activation function for layer i. Available options: tanh, sigmoid, linear, relu, lrelu100, elu. The index 'i' starts from 1.
  - **layer[i]_custom_activation** (string) - Optional - A custom mathematical expression for the activation function of layer i. Mutually exclusive with `layer[i]_activation`. The index 'i' starts from 1.
  - **componentCoeff** (number) - Optional - A coefficient for the component, used for normalization.
  - **dihedral** (object or array of objects) - Optional - Defines dihedral angle components used as inputs to the neural network.
    - **name** (string) - Required - The name of the dihedral component.
    - **componentCoeff** (number) - Optional - Normalization factor for the dihedral component.
    - **group1**, **group2**, **group3**, **group4** (object) - Required - Defines the atoms for the dihedral angle.
      - **atomNumbers** (array of integers) - Required - List of atom indices.

### Request Example
```json
{
  "name": "nn_output_1",
  "NeuralNetwork": {
    "output_component": 0,
    "layer1_WeightsFile": "dense_1_weights.txt",
    "layer1_BiasesFile": "dense_1_biases.txt",
    "layer1_activation": "tanh",
    "layer2_WeightsFile": "dense_2_weights.txt",
    "layer2_BiasesFile": "dense_2_biases.txt",
    "layer2_activation": "tanh",
    "componentCoeff": 180.0,
    "dihedral": [
      {
        "name": "001",
        "componentCoeff": 0.00555555555555555556,
        "group1": {"atomNumbers": [5]},
        "group2": {"atomNumbers": [7]},
        "group3": {"atomNumbers": [9]},
        "group4": {"atomNumbers": [15]}
      },
      {
        "name": "002",
        "componentCoeff": 0.00555555555555555556,
        "group1": {"atomNumbers": [7]},
        "group2": {"atomNumbers": [9]},
        "group3": {"atomNumbers": [15]},
        "group4": {"atomNumbers": [17]}
      }
    ]
  }
}
```

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

#### Response Example
```json
{
  "status": "success",
  "message": "MLCV component configured successfully."
}
```
```

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

### Target Distance File Format Example

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

An example of the multicolumn format for a target distance data file. It shows columns for distance, energy, and potentially other simulation data.

```text
#| 1 |  |  |  |
# | 0.0 | 0.1 | 1000 | 0
| 0.05 | 0.0012
| 0.15 | 0.0014
| … | …
| 99.95 | 0.0010
```

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

### Target Distance File Format Example

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Example of a multicolumn format for a target distance file. The first column represents the distance, and the second column represents the corresponding value.

```text
#|  1 |  |  |  |
# |  0.0 |  0.1 |  1000 |  0
|  0.05 |  0.0012
|  0.15 |  0.0014
|  … |  …
|  99.95 |  0.0010
```

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

### Configure Target Distribution File

Source: https://colvars.github.io/master/colvars-refman-namd.html

Example configuration for a target distribution file in the Colvars input.

```text
  targetDistFile    targetdist1.dat  
  ebMetaEquilSteps  500000  
} 
```

```text
#|  1 |  |  |  |   
# |  0.0 |  0.1 |  1000 |  0   
|  0.05 |  0.0012   
|  0.15 |  0.0014   
|  … |  …   
|  99.95 |  0.0010
```

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

### Two-Dimensional Grid File Header and Data Example

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Example of a multicolumn text file for a two-dimensional histogram of two dihedral angles. It shows a header for a periodic interval with specified bin size, followed by data rows.

```text
#  |  2  |  |  | | 
# |  -180.0 |  6.0 |  30 |  1 
#  |  -180.0  |  6.0  |  30  |  1 
|  -177.0 |  -177.0 |  8.97117e-06 |  | 
|  -177.0 |  -171.0 |  1.53525e-06 |  | 
|  …  |  …  |  …  |  | 
|  -177.0 |  177.0 |  2.442956-06 |  | 
|  -171.0 |  -177.0 |  2.04702e-05 |  | 
|  …  |  …  |  …  |  | 

```

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

### Configure Harmonic Walls

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Examples of setting up harmonic walls for one or two variables with specified force constants.

```text
harmonicWalls {  
  name  mywalls  
  colvars    dist  
  lowerWalls  22.0  
  upperWalls  38.0  
  lowerWallConstant  2.0  
  upperWallConstant 10.0  
}
```

```text
harmonicWalls {  
  name  mywalls  
  colvars       phi    psi  
  lowerWalls -180.0    0.0  
  upperWalls    0.0  180.0  
  forceConstant 5.0  
}
```

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

### GET /Colvars/list

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Retrieves a list of all input/configuration files currently loaded in the session.

```APIDOC
## GET /Colvars/list

### Description
Get a list of all input/configuration files loaded in this session.

### Method
GET

### Response
#### Success Response (200)
- **list** (sequence of strings) - List of file names
```

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

### One-Dimensional Grid File Header and Data Example

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Example of a multicolumn text file for a one-dimensional histogram. It includes header lines defining grid parameters like minimum value, width, and number of points, followed by data rows.

```text
#|  1 |  |  |  | 
# |  15 |  0.1 |  330 |  0 
|  15.05 |  6.14012e-07 |  |  | 
|  15.15  |  7.47644e-07  |  |  | 
|  … |  … |  |  | 
|  47.85  |  1.65944e-06  |  |  | 
|  47.95 |  1.46712e-06 |  |  | 

```

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

### Multidimensional Histograms Configuration

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

This example demonstrates the configuration of a two-dimensional histogram for distance and angle collective variables.

```APIDOC
## POST /colvars/histogram

### Description
Configures a multidimensional histogram to record the distribution of a set of collective variables. This is primarily for analysis and does not affect the simulation dynamics.

### Method
POST

### Endpoint
/colvars/histogram

### Parameters
#### Request Body
- **colvar** (object) - Required - Defines a collective variable to be included in the histogram. Can be specified multiple times for N-dimensional histograms.
  - **name** (string) - Required - The name of the collective variable.
  - **width** (number) - Required - The grid spacing for the variable.
  - **lowerBoundary** (number) - Optional - The lower boundary of the interval for the variable.
  - **upperBoundary** (number) - Optional - The upper boundary of the interval for the variable.
  - **distance** (object) - Configuration for a distance collective variable.
  - **dihedral** (object) - Configuration for a dihedral angle collective variable.
- **histogram** (object) - Required - Configuration for the histogram itself.
  - **name** (string) - Required - The name of the histogram.
  - **colvars** (string) - Required - A space-separated list of collective variable names to be included in the histogram.
  - **stepZeroData** (boolean) - Optional - Whether to include data from step zero.

### Request Example
```json
{
  "colvar": [
    {
      "name": "r",
      "width": 0.2,
      "upperBoundary": 20.0,
      "distance": {}
    },
    {
      "name": "theta",
      "width": 3.0,
      "dihedral": {}
    }
  ],
  "histogram": {
    "name": "hist2d",
    "colvars": "r theta"
  }
}
```

### Response
#### Success Response (200)
- **message** (string) - Confirmation message indicating successful configuration.

#### Response Example
```json
{
  "message": "Histogram configured successfully."
}
```
```

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

### Configure OPES with adaptive kernel bandwidth and PMF output

Source: https://colvars.github.io/master/colvars-refman-namd.html

This example demonstrates a full configuration for an OPES simulation, including defining dihedral collective variables and setting up the opes_metad block with adaptive kernel bandwidth, neighbor list, and PMF output options.

```text
colvarsTrajFrequency    500   
  
colvar {   
  name phi   
  lowerBoundary -180   
  upperBoundary 180   
  width 5.0   
  dihedral {   
    group1 {atomNumbers { 5 }}  
    group2 {atomNumbers { 7 }}  
    group3 {atomNumbers { 9 }}  
    group4 {atomNumbers { 15}}  
  }   
}   
  
colvar {   
  name psi   
  lowerBoundary -180   
  upperBoundary 180   
  width 5.0   
  dihedral {   
    group1 {atomNumbers { 7 }}   
    group2 {atomNumbers { 9 }}   
    group3 {atomNumbers { 15 }}   
    group4 {atomNumbers { 17 }}   
  }   
}   
  
opes_metad {   
  colvars phi psi   
  newHillFrequency 500   
  barrier 11.950286806883364   
  adaptiveSigma on   
  neighborList on   
  printTrajectoryFrequency 500   
  pmf on   
  pmfColvars phi psi   
  pmfHistoryFrequency 1000   
  outputEnergy on   
} 
```

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

### Example OPES Input Configuration

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

This configuration demonstrates setting up OPES with adaptive kernel bandwidth, neighbor list, and PMF calculation based on reweighting. It includes definitions for two colvars, phi and psi, and configures the opes_metad block with various parameters for PMF generation and trajectory output.

```plaintext
colvarsTrajFrequency    500   
  
colvar {
  name phi 
  lowerBoundary -180 
  upperBoundary 180 
  width 5.0 
  dihedral {
    group1 {atomNumbers { 5 }}
    group2 {atomNumbers { 7 }}
    group3 {atomNumbers { 9 }}
    group4 {atomNumbers { 15}}
  }
}
  
colvar {
  name psi 
  lowerBoundary -180 
  upperBoundary 180 
  width 5.0 
  dihedral {
    group1 {atomNumbers { 7 }}
    group2 {atomNumbers { 9 }}
    group3 {atomNumbers { 15 }}
    group4 {atomNumbers { 17 }}
  }
}
  
opes_metad {
  colvars phi psi 
  newHillFrequency 500 
  barrier 11.950286806883364 
  adaptiveSigma on 
  neighborList on 
  printTrajectoryFrequency 500 
  pmf on 
  pmfColvars phi psi 
  pmfHistoryFrequency 1000 
  outputEnergy on 
}

```

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

### cv colvar name get

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Gets the value of a given feature for this collective variable.

```APIDOC
## cv colvar name get

### Description
Get the value of the given feature for this colvar

### Method
Not applicable (command-line interface)

### Endpoint
Not applicable (command-line interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
- **state** (1/0) - State of the given feature

#### Response Example
None
```

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

### Two-Dimensional Histogram Grid File Example

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Example of a multicolumn text file for a two-dimensional histogram of dihedral angles. This format is used for periodic intervals and includes header and data rows.

```text
#  |  2  |  |  | | 
# |  -180.0 |  6.0 |  30 |  1 
#  |  -180.0  |  6.0  |  30  |  1 
|  -177.0 |  -177.0 |  8.97117e-06 |  | 
|  -177.0 |  -171.0 |  1.53525e-06 |  | 
|  …  |  …  |  …  |  | 
|  -177.0 |  177.0 |  2.442956-06 |  | 
|  -171.0 |  -177.0 |  2.04702e-05 |  | 
|  …  |  …  |  …  |  | 
```

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

### Configure gspathCV and gzpathCV

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Example configuration for defining progress along a path (gspathCV) and distance from a path (gzpathCV) using dihedral angles as CV components.

```text
colvar {  
  # Progress along the path  
  name gs  
  # Path defined by the CV space of two dihedral angles  
  gspathCV {  
    pathFile ./path.txt  
    dihedral {  
      name 001  
      group1 {atomNumbers {5}}  
      group2 {atomNumbers {7}}  
      group3 {atomNumbers {9}}  
      group4 {atomNumbers {15}}  
    }  
    dihedral {  
      name 002  
      group1 {atomNumbers {7}}  
      group2 {atomNumbers {9}}  
      group3 {atomNumbers {15}}  
      group4 {atomNumbers {17}}  
    }  
  }  
}  
  
colvar {  
  # Distance from the path  
  name gz  
  gzpathCV {  
    pathFile ./path.txt  
    dihedral {  
      name 001  
      group1 {atomNumbers {5}}  
      group2 {atomNumbers {7}}  
      group3 {atomNumbers {9}}  
      group4 {atomNumbers {15}}  
    }  
    dihedral {  
      name 002  
      group1 {atomNumbers {7}}  
      group2 {atomNumbers {9}}  
      group3 {atomNumbers {15}}  
      group4 {atomNumbers {17}}  
    }  
  }  
} 
```

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

### One-Dimensional Histogram Grid File Example

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Example of a multicolumn text file representing a one-dimensional histogram. It includes header information and data points with collective variable values and function values.

```text
#|  1 |  |  |  | 
# |  15 |  0.1 |  330 |  0 
|  15.05 |  6.14012e-07 |  |  | 
|  15.15  |  7.47644e-07  |  |  | 
|  … |  … |  |  | 
|  47.85  |  1.65944e-06  |  |  | 
|  47.95 |  1.46712e-06 |  |  | 
```

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

### Configure Target Distance File

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Example configuration block for setting up a target distance file in Colvars. Ensure the file format matches the specified width.

```text
targetDistFile	targetdist1.dat
  ebMetaEquilSteps	500000
}
```

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

### Example Usage of gspath and gzpath

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Illustrates how to configure the gspath and gzpath collective variables within a colvar block, specifying atoms and reference position files.

```APIDOC
colvar {
  # Progress along the path
  name gs
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path
  gspath {
    atoms {atomnumbers { 1 2 3 }}
    refPositionsFile1 string-00.pdb
    refPositionsFile2 string-01.pdb
    refPositionsFile3 string-02.pdb
    refPositionsFile4 string-03.pdb
    refPositionsFile5 string-04.pdb
  }
}
colvar {
  # Distance from the path
  name gz
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path
  gzpath {
    atoms {atomnumbers { 1 2 3 }}
    refPositionsFile1 string-00.pdb
    refPositionsFile2 string-01.pdb
    refPositionsFile3 string-02.pdb
    refPositionsFile4 string-03.pdb
    refPositionsFile5 string-04.pdb
  }
}
```

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

### Colvars Trajectory File Example

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Example of a Colvars trajectory file, which is a plain text file containing simulation data. The header line provides labels for columns like 'step', 'A', and 'E_rA'.

```text
#       step   A                     E_rA  
           0    1.42467449615693e+01  6.30982865292123e+02  
         100    1.42282559728026e+01  6.20640585041317e+02  
…
```

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

### Load Colvars configuration from file

Source: https://colvars.github.io/master/colvars-refman-namd.html

Loads a Colvars configuration file into the current NAMD session.

```tcl
cv configfile "colvars-file.in"
```

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

### Loading configuration from a string

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Directly injects configuration settings using a string.

```LAMMPS
fix_modify Colvars config "keyword { ... }"
```

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

### cv version

Source: https://colvars.github.io/master/colvars-refman-namd.html

Get the Colvars version string.

```APIDOC
## cv version

### Description
Get the Colvars version string.

### Method
GET

### Endpoint
N/A (Command Line Interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Response
#### Success Response (200)
- **version** (string) - Colvars version

### Response Example
```json
{
  "version": "20230801"
}
```
```

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

### GET /Colvars/printframe

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Returns the values that would be written to colvars.traj.

```APIDOC
## GET /Colvars/printframe

### Description
Return the values that would be written to colvars.traj.

### Method
GET

### Response
#### Success Response (200)
- **values** (string) - The values
```

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

### Configure Multiple-walker Metadynamics

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Example configuration for enabling multiple-walker metadynamics with file-based communication. Ensure the replicaUpdateFrequency is set to a value larger than newHillFrequency for optimal performance.

```text
metadynamics {  
  name mymtd  
  colvars x  
  hillWeight 0.001  
  newHillFrequency 1000  
  hillWidth 3.0  
  
  multipleReplicas    on  
  replicasRegistry       /shared-folder/mymtd-replicas.txt  
  replicaUpdateFrequency 50000  # Best if larger than newHillFrequency  
} 
```

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

### Example Usage of aspathCV and azpathCV

Source: https://colvars.github.io/master/colvars-refman-tinkerhp.html

Illustrates how to configure and use both aspathCV and azpathCV within a colvar configuration block, defining a path based on two dihedral angles.

```APIDOC
```colvar
colvar {
  # Progress along the path
  name as
  # Path defined by the CV space of two dihedral angles
  aspathCV {
    pathFile ./path.txt
    weights {1.0 1.0}
    lambda 0.005
    dihedral {
      name 001
      group1 {atomNumbers {5}}
      group2 {atomNumbers {7}}
      group3 {atomNumbers {9}}
      group4 {atomNumbers {15}}
    }
    dihedral {
      name 002
      group1 {atomNumbers {7}}
      group2 {atomNumbers {9}}
      group3 {atomNumbers {15}}
      group4 {atomNumbers {17}}
    }
  }
}

colvar {
  # Distance from the path
  name az
  azpathCV {
    pathFile ./path.txt
    weights {1.0 1.0}
    lambda 0.005
    dihedral {
      name 001
      group1 {atomNumbers {5}}
      group2 {atomNumbers {7}}
      group3 {atomNumbers {9}}
      group4 {atomNumbers {15}}
    }
    dihedral {
      name 002
      group1 {atomNumbers {7}}
      group2 {atomNumbers {9}}
      group3 {atomNumbers {15}}
      group4 {atomNumbers {17}}
    }
  }
}
```
```

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

### cv colvar name width

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Gets the width of this collective variable.

```APIDOC
## cv colvar name width

### Description
Get the width of this colvar

### Method
Not applicable (command-line interface)

### Endpoint
Not applicable (command-line interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
- **width** (float) - Value of the width

#### Response Example
None
```

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

### cv colvar name value

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Gets the current value of this collective variable.

```APIDOC
## cv colvar name value

### Description
Get the current value of this colvar

### Method
Not applicable (command-line interface)

### Endpoint
Not applicable (command-line interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
- **value** (float or array) - Current value; matches the colvar dimensionality

#### Response Example
None
```

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

### Periodic Boundary Conditions (PBC) Handling

Source: https://colvars.github.io/master/colvars-refman-namd.html

Explains the default minimum-image convention for distance vectors and how the `forceNoPBC` keyword can be used to ignore PBCs for specific calculations.

```APIDOC
## Periodic Boundary Conditions (PBC) Handling

### Description
This section describes how Colvars applies periodic boundary conditions (PBCs) to collective variable calculations, particularly for distance-based components. By default, distance vectors use the minimum-image convention. The `forceNoPBC` keyword allows overriding this behavior.

### Keywords
- **forceNoPBC** (boolean) - Default: no
  If set to `yes`, PBCs are ignored when calculating distances. This is useful for cases where the minimum-image convention might yield incorrect results, such as measuring distances within a single large molecule that spans periodic boundaries.

### Example: Ignoring PBCs in Distance Calculation
```colvars
colvar {
  name d
  distance {
    forceNoPBC yes
    group1 { ... }
    group2 { ... }
  }
}
```
```

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

### cv colvar name type

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Gets the type description of this collective variable.

```APIDOC
## cv colvar name type

### Description
Get the type description of this colvar

### Method
Not applicable (command-line interface)

### Endpoint
Not applicable (command-line interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
- **type** (string) - Type description

#### Response Example
None
```

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

### Loading Initial ABF Data

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Configuration for loading initial gradient and sampling files to set up the ABF algorithm's initial state.

```APIDOC
## Loading Initial ABF Data

### Description
This option allows the ABF algorithm to initialize its state by reading gradient and sampling files at startup. It is useful for combining data from different simulation regions or adjusting colvar boundaries.

### Parameters
#### Input Prefix
* **inputPrefix** (string) - Specifies the prefix for gradient (`.grad`) and sampling (`.count`) files to be read at startup. The data from all provided files is combined.

### Notes
* The grid definition (min/max values, width) of the input files need not match the current run's grid.
* Not recommended to switch to a smaller width, as it may leave bins empty.
* This option is NOT compatible with reading data from a restart file.

### Request Example
```json
{
  "inputPrefix": "my_abf_data"
}
```

### Response
#### Success Response (200)
* **status** (string) - Indicates successful loading of initial ABF data.

#### Response Example
```json
{
  "status": "Initial ABF data loaded successfully."
}
```
```

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

### POST /Colvars/molid

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Get or set the molecule ID on which Colvars is defined (VMD only).

```APIDOC
## POST /Colvars/molid

### Description
Get or set the molecule ID on which Colvars is defined (VMD only).

### Method
POST

### Parameters
#### Request Body
- **molid** (integer) - Optional - New molecule ID; -1 means undefined

### Response
#### Success Response (200)
- **molid** (integer) - Current molecule ID
```

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

### Define gspath and gzpath using atomic coordinates

Source: https://colvars.github.io/master/colvars-refman-gromacs.html

Illustrates the configuration of gspath and gzpath components using reference PDB files for atomic coordinate-based path definition.

```text
colvar {  
  # Progress along the path  
  name gs  
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)  
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path  
  gspath {  
    atoms {atomnumbers { 1 2 3 }}  
    refPositionsFile1 string-00.pdb  
    refPositionsFile2 string-01.pdb  
    refPositionsFile3 string-02.pdb  
    refPositionsFile4 string-03.pdb  
    refPositionsFile5 string-04.pdb  
  }  
}  
colvar {  
  # Distance from the path  
  name gz  
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)  
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path  
  gzpath {  
    atoms {atomnumbers { 1 2 3 }}  
    refPositionsFile1 string-00.pdb  
    refPositionsFile2 string-01.pdb  
    refPositionsFile3 string-02.pdb  
    refPositionsFile4 string-03.pdb  
    refPositionsFile5 string-04.pdb  
  }  
} 
```

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

### fix_modify Colvars frame

Source: https://colvars.github.io/master/colvars-refman-lammps.html

Gets or sets the current frame number (VMD only).

```APIDOC
## fix_modify Colvars frame

### Description
Get or set current frame number (VMD only).

### Parameters
#### Request Body
- **frame** (integer) - Optional - Frame number

### Response
#### Success Response (200)
- **frame** (integer) - Frame number
```

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

### Configure Multiple-Walker Metadynamics

Source: https://colvars.github.io/master/colvars-refman-vmd.html

Example configuration for multiple-walker metadynamics using file-based communication. Ensure 'multipleReplicas' is set to 'on' and 'replicasRegistry' points to a shared file.

```colvars
metadynamics {
  name mymtd
  colvars x
  hillWeight 0.001
  newHillFrequency 1000
  hillWidth 3.0
  
  multipleReplicas       on
  replicasRegistry       /shared-folder/mymtd-replicas.txt
  replicaUpdateFrequency 50000 	# Best if larger than newHillFrequency
}
```

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

### GET /cv/colvar/{name}/value

Source: https://colvars.github.io/master/colvars-refman-namd.html

Retrieves the current value of a collective variable.

```APIDOC
## GET /cv/colvar/{name}/value

### Description
Get the current value of this colvar.

### Parameters
#### Path Parameters
- **name** (string) - Required - The name of the colvar

### Response
#### Success Response (200)
- **value** (float or array) - Current value; matches the colvar dimensionality
```

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

### cv units [units]

Source: https://colvars.github.io/master/colvars-refman-namd.html

Get or set the current Colvars unit system.

```APIDOC
## cv units [units]

### Description
Get or set the current Colvars unit system.

### Method
GET/SET

### Endpoint
N/A (Command Line Interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **units** (string) - Optional - The new unit system.

### Response
#### Success Response (200)
- **units** (string) - The current unit system

### Response Example
```json
{
  "units": "Angstrom,amu,kcal/mol"
}
```
```

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

### Define aspath and azpath collective variables

Source: https://colvars.github.io/master/colvars-refman-namd.html

Example configuration for tracking progress along (aspath) and distance from (azpath) a path defined by five reference PDB files.

```text
colvar {  
  # Progress along the path  
  name as  
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)  
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path  
  aspath {  
    atoms {atomnumbers { 1 2 3 }}  
    refPositionsFile1 string-00.pdb  
    refPositionsFile2 string-01.pdb  
    refPositionsFile3 string-02.pdb  
    refPositionsFile4 string-03.pdb  
    refPositionsFile5 string-04.pdb  
  }  
}  
  
colvar {  
  # Distance from the path  
  name az  
  # The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)  
  # Use atomic coordinate from atoms 1, 2 and 3 to compute the path  
  azpath {  
    atoms {atomnumbers { 1 2 3 }}  
    refPositionsFile1 string-00.pdb  
    refPositionsFile2 string-01.pdb  
    refPositionsFile3 string-02.pdb  
    refPositionsFile4 string-03.pdb  
    refPositionsFile5 string-04.pdb  
  }  
}
```

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

### cv patchversion

Source: https://colvars.github.io/master/colvars-refman-namd.html

Get the Colvars patch version number (used for bugfixes only).

```APIDOC
## cv patchversion

### Description
Get the Colvars patch version number (used for bugfixes only).

### Method
GET

### Endpoint
N/A (Command Line Interface)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Response
#### Success Response (200)
- **version** (string) - Colvars version

### Response Example
```json
{
  "version": "20230801"
}
```
```