[gmx-users] Can g_wham support using different temperature for different windows?
ljggmx at yahoo.com.sg
Tue Feb 22 02:32:57 CET 2011
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!
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