Dear Dr.Justin There is not any answer?
On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Yes,you are right > I need to do more sampling.But the second attached file was just to > transfer my mean :) > My final PMF curve is the first attached file. > > Sorry for asking more questions.. > > Regarding my notes about windowses in last email and looking at FIRST > attached file: > Which one is my starting point? > 0.18 (with negative value ) OR 0.03 (with about zero value) OR the average > in that region? > > Because there is a difference about 0.5 kcal/mol . > Thanks in advance > > > > > > On Mon, May 30, 2011 at 7:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> >> >> mohsen ramezanpour wrote: >> >>> Thank you. >>> >>> no,I think the problem is not zero point. >>> Actually I maean some thing like this one.please have a look at new >>> attached file. >>> I just added 3 new windows in 0.3 - 0.8 >>> But the whoe of my curve shifted upward. >>> >>> There is another question: >>> Actually I pulled my drug from 0.18 - 3.18 >>> then,extracted some windows.umbrella0 for 0.18 and umbrella20 for 3.18 >>> Besides as we know drug is oscilating in it's windows. >>> so ,it must cover places as like as 0.12 and 3.22 too. >>> Am I right? >>> >>> >> Possibly. Harmonic potentials allow for oscillation. The amount by which >> the position shifts is a function of both the force constant you apply and >> the nature of the interactions within the system. >> >> >> But looking at curve it seems my drug couln't cover the region around >>> 0.18 >>> besides it ha covered completely(untill 0.03) the region around 0.18 >>> >>> What is the problem? >>> >>> Since I started from 0.18 (which energy is negative there),I am in doubt >>> about starting point. >>> Because it can be eighter 0.03 OR 0.18 >>> >>> >> All of this appears to be a consequence of poor sampling. You have >> several flat locations in both the PMF curves, indicating absolutely no >> sampling in that region. Your histograms should show you this, as well. >> You need more windows and more time in each. Based on what you've shown, >> your simulations are simply unconverged. >> >> >> -Justin >> >> -- >> ======================================== >> >> 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 >> > >
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