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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