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<div class="gmail_quote">On Thu, Feb 23, 2012 at 12:00 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">Dear Justin and Gmx Users,<br> I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why?<br>
</blockquote><br></div>The system at hand was very robust and as such, complete restraints were not necessary. Please do not adhere strictly to the umbrella sampling tutorial; there are elements of it that may not be generally applicable (and I'm fairly sure there are warnings of this in the tutorial). It is a simple example designed to provide the conceptual and practical basis for such simulations.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window?<br> <br></blockquote>
<br></div>Do what makes sense in your case. Typically, position restraints are applied during equilibration.<br><br>-Justin<br></blockquote>
<div> </div>
<div>Maybe I asked my qestion not directly. Why during the equilibration of your system (tutorial) NPT before umbrella sampling in each window you restarined only Chain B like in further umbrella samplin (your mdp files of NPT and MD are the same) instead of restraining all chains as it should be during the equilibration?</div>
<div> </div>
<div>Steven</div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><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>==========<span class="HOEnZb"><font color="#888888"><br>
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