metadynamics trajectory analysis by pyemma
This is an example for (issues)[markovmodel/PyEMMA#1014 (comment)].
2017.08.29, asking for help from @fabian-paul
metadynamics simulation
I select two distance between the center of mass of atom groups as collective variables (CVs), and then run using well-temper method with Gromacs, seeing plumed.dat.
After simulation, I got these following files:
- CVS, which contain CVs as time evolution.
- HILLS_CVS, which contain the bias added during the simulation
- fes.dat, which generated by run plumed driver method.
For my understanding, I try to employ the tram in pyemma to analysis this metadynamics trajectory.
The ipython notebook is at emma.ipynb or gist