Comparison of protein root mean square deviations (RMSD) between coarse-grained and atomistic simulations.

<p>RMSDs of transmembrane helix backbone beads determined from 100 coarse-grained (CG) homodimerization simulations (initial 500 ns) in POPC membranes (for systems where no interaction energies between both monomers were observed until 1 <i>μs</i>, shown in light grey). The average RMSDs of CG simulations are colored in red for CXCR4, green for CCR5, and blue for CCR2. The RMSD curves for atomistic simulations (CHARMM36 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006062#pcbi.1006062.ref111" target="_blank">111</a>] for CXCR4 and CHARMM36m [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006062#pcbi.1006062.ref116" target="_blank">116</a>] for CC chemokine receptors) of corresponding chemokine receptor monomers in POPC membranes, shown in black, were calculated by converting the atomistic simulation frame-by-frame (time step of 100 ps) to the Martini2.2 force field in order to enable a direct comparison to the CG simulations. The data for CXCR4 was taken from our previous study [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006062#pcbi.1006062.ref047" target="_blank">47</a>].