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 <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@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@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists