<br><br>
<div class="gmail_quote">On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br><br>Steven Neumann wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im"><br><br>On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Steven Neumann wrote:<br><br> Hi Justin,<br> As you advised I reduced number of my windows and I obtined<br> histogram:<br></div> <a href="http://speedy.sh/2b9dT/histo.__JPG" target="_blank">http://speedy.sh/2b9dT/histo._<u></u>_JPG</a>
<div class="im"><br> <<a href="http://speedy.sh/2b9dT/histo.JPG" target="_blank">http://speedy.sh/2b9dT/histo.<u></u>JPG</a>><br> Which looks really good.<br> The corresponding profile:<br></div>
<a href="http://speedy.sh/y8Ssz/__profile.JPG" target="_blank">http://speedy.sh/y8Ssz/__<u></u>profile.JPG</a>
<div class="im"><br> <<a href="http://speedy.sh/y8Ssz/profile.JPG" target="_blank">http://speedy.sh/y8Ssz/<u></u>profile.JPG</a>><br> I do not understand it. Does my deltaG of binding correspond to<br>
everything above 0 kcal/mol which is 6 kcal/mol?<br> <br><br> DeltaG = the free energy difference between the final and initial<br> states. So that's up to you to decide. Your curve is rather rough<br>
and the energy minimum potentially still ill-defined. The<br> histograms indicate that the sampling overlap is likely fine, you<br> just may need a bit more sampling in each window to smooth things<br> out. Also make use of the error estimates that g_wham can provide;<br>
they can be quite informative (and necessary).<br><br> -Justin<br><br><br> Thank you Justin. In each window I run the simulation of 10 ns. Do you think that making it 20 ns will make the profile more smooth?<br> <br>
</div></blockquote><br>It's no use to blindly guess. It's up to you to assess the convergence of your simulations and decide on an appropriate time frame.<span class="HOEnZb"><font color="#888888"><br><br>-Justin</font></span>
<div class="HOEnZb">
<div class="h5"><br> </div></div></blockquote>
<div>Thank you Justin. Is there any way to find out after deltaG the entropic contribution to binding free energy?</div>
<div> </div>
<div>Steven</div>
<div> </div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="HOEnZb">
<div class="h5"><br>-- <br>==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>==============================<u></u>==========<br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br></div></div></blockquote></div><br>