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

[Jianguo Li]

Thanks Justin.
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...

best regards,
Jianguo






________________________________
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 
different windows?



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.

-Justin

> Cheers,
> Jianguo
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110222/3b941f8f/attachment.html>