Thank you for your reply<br><br>Actually my system is not the same as tutorial.<br>I tried to obtain protein-drug delta G.<br>I obtained that.<br>Yes,you are right,since I don't have good computaional systems I couldn't run more than 1 ns for each windows.<br>
<br>when there are some minimum and maximum in our curve ,How do I must evaluate Delta G?<br>the difference between minimum and maximum values OR difference between values corresponding to <br>0 and last windows(where they must be converged(be flatted))?<br>
<br>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.<br>Is not it strong(wonderfull?)?<br><br><div class="gmail_quote">On Mon, May 30, 2011 at 6:57 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr.Justin<br>
<br>
Regarding to PMF curve which resulted from Umbrella sampling:<br>
I obtained the following curve.<br>
Dose it mean?Because it is not similar to yours in tutorial :(<br>
if yes,please let me know what is the Delta G value approximately?<br>
Because I don't know difference between which points is my Delta G.There are some points with negative values,<br>
and there are a pick (hill like region ) before being converged at high values!<br>
</blockquote>
<br></div></div>
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.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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