A package for the analysis of simulations performed using OpenFE (more specifically .nc files created by OpenMMTools MultiStateReporter).
This package provides a MDAnalysis Reader to start to explore your trajectory data:
import MDAnalysis as mda
from openfe_analysis import FEReader
# a "simulation.nc" file contains multiple replicas, so we must choose which of these we load
# provide either a state (following a single lambda state) or replica (following a particular replica) id (typically 0-10)
u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, state=0)For example to convert your trajectory to a different format for visualisation:
import MDAnalysis as mda
from openfe_analysis import FEReader
with mda.Writer('out.xtc', n_atoms=len(u.atoms)) as w:
for ts in u.trajectory:
w.write(u.atoms)Installation is done via the conda package manager, simply:
conda install -c conda-forge openfe-analysis
For further guidance on using the conda package manager, please consult our installation guide