[gmx-users] Can g_wham support using different temperature for different windows?

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 22 02:35:37 CET 2011

Jianguo Li wrote:
> 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!

A more straightforward approach is to (1) add more sampling windows or (2) 
increase the force constant in regions where there's poor sampling, or perhaps both.


> Cheers,
> Jianguo


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list