Publications Details

Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2

Rempe, Susan R.; Priest, Chad; Vangordon, Monika R.; Rempe, Caroline; Stevens, Mark J.; Rick, Steve

Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.