Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility

Snapshots from MD simulations (with umbrella sampling and metadynamics) of
respiratory complex I. Only subunits ND1, NDUFS2 and NDUFS7 (with the membrane spanning N-terminus
truncated) and rotenone are shown in binding mode (see Fig. 2 of main paper): 

1) ROT1:        configurations/rot1.pdb
2) pre-redox:   configurations/rot1.5.pdb
3) ROT2:        configurations/rot2.pdb

Force-field and topology files in GROMACS format:

4) Bonded parameters:           parameters/rotenoids_ffBonded.itp
5) Rotenone:                    parameters/rot.itp
6) Dehydrated derivative:       parameters/dehyd_rot.itp