Dear Christian and Giacomo,
Thanks for your replies.
I contacted the author of GaMD, Prof. Yinglong Miao about the method. It is based on a similar mathematical formalism of the bias potential of conformational flooding. However, GaMD smooths the potential energy surface without the requirement of predefined collective variables. Also, it provides rigorous ways to re-weight both thermodynamics and kinetics from the simulations. All the information is on the website in my previous post.
I don’t know about the intricacies of the development process, which is great, btw. But, I do think that the implementation of this method could be useful for the community. Especially to avoid jumping to other software (NAMD, AMBER) and keep the reproducibility. That’s why my question about gromacs-gamd in Github because it looked like an independent development branch.
Best,
-Yasser