On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul <[email protected]> wrote:
> > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> There is not any answer? >> >> > Please have a bit of patience. I'm not your personal answer service. You > just happened to catch me at a good time this morning and I was able to > respond quickly. I have my own work to do, you know. Thanks for your reply No Dr.Justin,I didn't mean this by my question.It was your favour replying to my questions. I just thought my question is not logical OR it is answer is not difficult And I must review articles in this field.just this. > > > >> On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour < >> [email protected] <mailto:[email protected]>> >> wrote: >> >> Yes,you are right >> I need to do more sampling.But the second attached file was just to >> transfer my mean :) >> > > Always provide complete information. I can't get in your head to know > everything you're thinking. If you want free help, make it easy to help > you. Hack job files wind up causing confusion and delaying an answer rather > than providing you with one. Yes,You are right > > > 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? >> >> > I have no idea. Watch your trajectories and see what your ligand is doing > at these points. Presumably you have a window in which the ligand is bound > in the protein's active/receptor site, and perhaps after some simulation the > position moves to arrive at its energy minimum. In general, from a PMF > curve, the highest point (as long as it's stable) minus the lowest point is > your DeltaG. aha! > > > Because there is a difference about 0.5 kcal/mol . >> > > So there are some energetic differences in these windows. Watch the > trajectories to figure out why. > > Sure > > -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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