<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Thanks Justin.<br>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. <br><br>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...<br><br>best
regards,<br>Jianguo<br><br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 22 February 2011 09:35:37<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Can g_wham support using different temperature for different windows?<br></font><br><br><br>Jianguo Li wrote:<br>> Dear all,<br>> <br>> 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?<br>> <br>> 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?<br>> <br>> Btw, I am using Martini CG model.<br>> <br>> Any suggestions will be highly appreciated, thank you!<br>> <br><br>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.<br><br>-Justin<br><br>> Cheers,<br>>
Jianguo<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests
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