In this enhanced sampling method the bias potential is estimated from a model probability distribution.
The relative height of each island is estimated on-the-fly using:
The code for this algorithm can be found at GAMBES.cpp , it is compatible with PLUMED v2.7-dev.
- First run unbiased molecular dynamics simulations from at least one known state and for all known states.
- Using the GAMBES-module.ipynb code, fit a Gaussian Mixture Model to your state using any number of descriptors.
- The final file generated using the notebook is an input for GAMBES in PLUMED. Generate similar files for every known state of interest and name them as < file-name >.0 , < file-name >.1, ... , < file-name >.m where 0,1,...,m are your states. This < file-name > is an input for GAMBES.
- Copy GAMBES.cpp in a folder containing your plumed input, the states generated < file-name >.* and all other necessary files for running your system.
- Run the simulation.