<div>Thank you Justin, I will read it for sure and come back to my simulations!</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Thu, Nov 17, 2011 at 1:25 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">Hi Justin,<br> I am sorry for so many questions but I do not understand something.<br>First we run the simulation of pulling Chain A from ChainB with constant force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We extract windows as we discussed and then run simulations with those configurations as a starting point. I saw the trajectory of one of these simulations and it looks like normal MD simulation. My question is: Why do we have in mdp file still pull code as we do not pull protein chain any more? Pull rate is set to zero but force is still applied... why? Is this code just used to extract pullf.xvg and pullx.xvg which does not change too much?<br>
I would appreciate the explanation as without undesratnding the basics its not good to do any simulation like this.<br> <br></blockquote><br></div>Have you read the WHAM paper, or the one specific for g_wham, or perhaps papers about umbrella sampling in general? You should start there before diving in to doing the simulations.<br>
<br>The harmonic force applied in the SMD and US simulations is simply a biasing force to make something happen. With a non-zero pull_rate, motion in a particular direction is forced to happen. With a pull_rate of zero, the COM distance is simply restricted - the biasing force maintains the COM distance between the two defined species, while allowing it to oscillate according to a harmonic force defined by pull_k1. Thus you establish sampling overlap between neighboring windows along the reaction coordinate.
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<div class="h5"><br><br>-Justin<br><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>
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