Thank you Justin!<br><br>
<div class="gmail_quote">On Mon, Feb 13, 2012 at 2:44 PM, 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">
<div class="im"><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">Thank you Justin. I run my pulling using two force constant for pulling. K1=100 and K1=200<br>Please, see attached plots of force vs time. Is there any criteria to adjust pulling constant? Would you suggest running it for a longer time?<br>
</blockquote><br></div>I know of no systematic study for choosing a force constant. Guessing wildly at what's going on, I'd say you need longer simulations as it appears you have only just caused dissociation towards the end of the 500 ps.<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Steven
<div class="im"><br>On Mon, Feb 13, 2012 at 1:11 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> Dear Gmx Users,<br> Is it always required to restrained positions of the protein<br> while pulling your ligand? My system is made of 10 ligands<br> attached to my protein surface. I am pulling one of them.<br>
<br><br> No, it is not required. I assume you've gotten this idea from my<br> tutorial - the restraints there were used for a very specific<br> purpose (detailed in the paper linked from the tutorial).<br><br><br>
I have just seen trajectory of pulling my ligand without<br> restraining positions of protein and 9 remaining ligands. My<br> ligand while pulling also pulled the protein with itself (for 1<br> nm distance) and then splited. Is is this approach more reliable?<br>
<br><br> If your goal is umbrella sampling, you need only generate a series<br> of reasonable starting configurations along a defined reaction<br> coordinate. The absolute positions are irrelevant; it is the<br>
relative distance that matters.<br><br> -Justin<br><br></div> -- ==============================<u></u>__==========
<div class="im"><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></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br>
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<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>
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