[gmx-users] Can g_wham support using different temperature for different windows?
ljggmx at yahoo.com.sg
Tue Feb 22 02:49:47 CET 2011
I tried your suggestions by either increase more windows and change the force
constant, but it seems the samplings are still bad in some windows. When I did
pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got
different configurations at certain reaction coordinates. And the windowed
umbrella sampling seems depends strongly on the initial configurations in that
window. Therefore I got different PMFs using pulling in (0 0 1) direction and
reverse pulling in （0 0 -1) direction.
In my simulation, I exert constraints on phosphate atoms in z direction, so
there is no lipid flip-flop and the membrane will be stable at high
temperatures. Then I am thinking of increasing temperature in those bad windows
to enhance sampling...
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 22 February 2011 09:35:37
Subject: Re: [gmx-users] Can g_wham support using different temperature for
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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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