Thank you for your reply Actually my system is not the same as tutorial. I tried to obtain protein-drug delta G. I obtained that. Yes,you are right,since I don't have good computaional systems I couldn't run more than 1 ns for each windows.
when there are some minimum and maximum in our curve ,How do I must evaluate Delta G? the difference between minimum and maximum values OR difference between values corresponding to 0 and last windows(where they must be converged(be flatted))? Besides when I add a new windows in places which there are not enough sampling ,a vertical shift is resultedin the whole of my curve. Is not it strong(wonderfull?)? On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul <[email protected]> wrote: > > > mohsen ramezanpour wrote: > >> Dear Dr.Justin >> >> Regarding to PMF curve which resulted from Umbrella sampling: >> I obtained the following curve. >> Dose it mean?Because it is not similar to yours in tutorial :( >> if yes,please let me know what is the Delta G value approximately? >> Because I don't know difference between which points is my Delta G.There >> are some points with negative values, >> and there are a pick (hill like region ) before being converged at high >> values! >> > > Please clarify - is this the result you obtained from running the tutorial? > If this is some other system, I'm not going to try to guess what your > result should look like. The curve is a bit rough, so maybe you need a bit > more sampling to smooth it out, but complex PMF curves are not necessarily > wrong. The result will depend on the interactions your system experiences > along the reaction coordinate. There may be local minima and other > metastable states along the way. > > -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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