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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.


Chad Priest, Monika R VanGordon, Caroline Rempe, Mangesh I Chaudhari, Mark J Stevens, Steve Rick, Susan B Rempe. Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2. Methods in molecular biology (Clifton, N.J.). 2021;2191:17-28

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PMID: 32865736

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