Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows?
If g_wham cannot deal with the bias due to using different T, I may need to do REMD in those windows. But that will be very expensive computationally. Anybody have an idea of enhancing sampling in those windows? Btw, I am using Martini CG model. Any suggestions will be highly appreciated, thank you! Cheers, Jianguo
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