<div>Hi Justin,</div>
<div> </div>
<div>I am sorry for so many questions but I do not understand something.</div>
<div>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?</div>
<div>I would appreciate the explanation as without undesratnding the basics its not good to do any simulation like this.</div>
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<div>Thank you</div>
<div> </div>
<div>Steven</div>
<div><br> </div>
<div> </div>
<div> </div>
<div>Are my questions to trivial or noones knows? Please, help!<br><br></div>
<div class="gmail_quote">On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>Hi GMX Users,</div>
<div> </div>
<div>I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other?</div>
<div> </div>
<div>The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations:</div>
<div> </div>
<div>0 - 0.50</div>
<div>50 - 0.52</div>
<div>100 - 0.51</div>
<div>150 - 0.51</div>
<div>200 - 0.62</div>
<div>250 - 2.21</div>
<div>....</div>
<div>500 - 5.48</div>
<div> </div>
<div>My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? </div>
<div>And the last thing - is it required to use frames till 189 as the COM varies in this area?</div>
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<div>Thank you!</div>
<div> </div><font color="#888888">
<div>Steven</div></font></blockquote></div><br>