The similar files for wt can be assesed at http://www.freefilehosting.net/umbrellawt I expected wild type binding energy to be less than mutant The command used for g_wham is g_wham_mpi_4.5.4 -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg -hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac I get the values exactly opposite to my expectation and unable to find out where I am wrong please suggest. Shahid Nayeem
On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem <[email protected]> wrote: > I have added some new windows in mutant umbrella sampling which removes > the sampling gap around 4 nm. Also I sampled more windows in the initial > COM distance in the hope that I get energy minimum of profile well defined. > I also did boot strapping for error estimates. The files can be assessed at > http://www.freefilehosting.net/umbrellamut > > > On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul <[email protected]> wrote: > >> >> >> shahid nayeem wrote: >> >>> The attached profile.xvg and histo.xvg are here. >>> sorry for sending earlier mail without attachments >>> Shahid Nayeem >>> >>> On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem <[email protected]<mailto: >>> [email protected]>> wrote: >>> >>> As suggested by you I added some new window and extended some >>> simulation and I got the attached profile and histo file. Please see >>> these files. Experimentally it is known that wt protein-protein >>> interaction is stronger than the mutants. But I get here is reverse. >>> what could be the possible reason for it. My profile.xvg and >>> histo.xvg are right or they need more improvement. >>> >> >> I wouldn't base any conclusions off of them. You have a sampling gap at >> just over 4 nm in the mutant simulations. More importantly, you do not >> have a defined energy minimum in the mutant windows so it is impossible to >> calculate a reliable value for DeltaG. Moreover, in the absence of any >> error estimates, you can't make any conclusions about these data. g_wham >> can generate error bars for you; I'd suggest you do it. >> >> -Justin >> >> Shahid Nayeem >>> >>> >>> On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> >>> >>> shahid nayeem wrote: >>> >>> Thanks. But Does that mean that I should look in pullf.xvg >>> of each window and see whether the value is converged or >>> not. If not then I should extend the simulation. >>> >>> >>> I've already made numerous suggestions. The value in pullf.xvg >>> is a consequence of the nature of the system. Looking at the >>> interactions between your proteins, the stability of those >>> proteins, etc. is far more informative, like you would for any >>> simulation (even those that do not make use of the pull code). >>> >>> >>> -Justin >>> >>> -- ==============================**__========== >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>> >>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================**__========== >>> -- gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> >>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> >>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> Please search the archive at >>> >>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >>> >>> <mailto:gmx-users-request@**gromacs.org<[email protected]> >>> >. >>> Can't post? Read >>> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >>> >>> >> -- >> ==============================**========== >> >> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================**========== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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 [email protected]. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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