Definition of custom collective variables¶

Apart from the List of collective variables already implemented in the metafalcon package, it is possible to define own variables to be used as metadynamics CVs. For each new CV, it is necessary to provide a file that contains two functions, customcv() for the calculation of the variable values from the current coordinates and dcustomcv() for the calculation of its gradient. In order to copy a template cvcustom.py for the definition of these two functions into your working directory, run:

metaFALCON custom

It is important that function names, arguments and returns are not modified. Modifications should only occur in the designated places in customcv():

### modify the following code
custom = 0.0
### end modify

and in dcustomcv():

### modify the following code
dcustom = np.zeros_like(coords)
### end modify

However, you can create help functions or import other modules within the cvcustom module without any problems. Additional parameters needed for the calculation can be provided in meta-config.json using the "parameters" keyword:

{
  "name": "user-defined variable",
  "type": "custom",
  "filename": "cvcustom",
  "width": 1.0,
  "parameters": {
    "key1": value1,
    "key2": value2,
    ...
  }

The dictionary that contains "key1" and "key2" is given to customcv() and dcustomcv() through the prm argument. The "filename" keyword is optional and only needed, if files other than cvcustom.py are used, for example because multiple user-defined variables are used in the same simulation.

In the metafalcon package, lengths and energies are internally handled in atomic units. If a different unit of the variable should be used in the user input and output (e.g. the Gaussian width given in the meta-config.json file), a conversion factor is needed. Edit the line

au2unit = 1.0

so that au2unit by multiplication converts atomic units into the unit of your variable. For example, if you define a bond length in Angstrom, use:

au2unit = 0.529