LD is funded by a NC3Rs studentship and was also a Cephalosporin Scholar at Lady Margaret Hall, Oxford. We thank the Advanced Research Computing (ARC) facility, the EPSRC UK National Service for Computational Chemistry Software (NSCCS) at Imperial College London (grant no. EP/J003921/1) and the ARCHER UK National Supercomputing Services for computer time granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://www.hecbiosim.ac.uk), supported by EPSRC (grant no. EP/L000253/1). H.K. acknowledges a research fellowship from the Alfred Benzon Foundation. Work in PCB's laboratory is supported by the MRC (MR/M000435/1) and the BBSRC (BB/M006395/1).

The topology (gro) and trajectory (xtc) files for multiscale - coarse-grained (CG) and atomistic (AT) molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer. The coarse grained simulations are 10 microseconds long and the trajectories have 1 frame saved at every 10 ns, while the atomistic simulations are 100 ns long and have 2 frames saved at every nanosecond.