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 <[email protected]> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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