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.
CITATION STYLE
Priest, C., VanGordon, M. R., Rempe, C., Chaudhari, M. I., Stevens, M. J., Rick, S., & Rempe, S. B. (2021). Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2. In Methods in Molecular Biology (Vol. 2191, pp. 17–28). Humana Press Inc. https://doi.org/10.1007/978-1-0716-0830-2_2
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