<div>Hi Justin</div>
<div>Should I try to do position restraint at 500k and then full MD simulation.</div>
<div>shahid<br><br> </div>
<div><span class="gmail_quote">On 4/27/10, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file<br>
<br></blockquote><br></span><snip><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>ref_t = 300 300<br></blockquote><br>Here, you're equilibrating at 300 K...<br><br><snip><br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">ref_t = 500 500<br></blockquote><br>and here, you're running MD at 500 K, without any equilibration in between. That could be a problem, but more likely, the high temperature is simply causing the structure to break down. Short helices are usually not stable in isolation, and heating them to extreme conditions will probably accelerate this process. The various results you're seeing with different helices may just reflect that you haven't simulated long enough to see convergence in the structural features, but from what you've described, I expect what you're seeing is entirely normal, and almost predictable.<br>
<span class="sg"><br>-Justin</span>
<div><span class="e" id="q_1283f7b3b6be9f47_3"><br><br>-- <br>========================================<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 onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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