gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support
Fig 5
Residue-residue distance distributions in a simulated ensemble of HIV gp41.
DEER spectroscopy was used to measure distance distributions between two monomers of the gp41 trimer. Thus, each residue designates a monomer-monomer residue pair. Panels A-E show plots for the 5 restrained residues in the HIV trimer: 106, 173, 202, 306, and 542 respectively. Discretized DEER distance distributions are plotted in green, and simulation results are plotted in blue bars. The simulation ensemble shows good convergence to the measured values.