<div>Hi!</div>
<div>So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to handle the simulated annealing for the appended NMR group?</div>
<div>Thanks</div>
<div>Jayant James</div>
<div> </div>
<div><span lang="EN">
<p>; Berendsen temperature coupling is on in two groups</p>
<p>Tcoupl = berendsen</p>
<p>tc-grps = Protein Non-Protein </p>
<p>tau_t = 0.1 0.1 </p>
<p>ref_t = 300 300 </p>
<p>; Energy monitoring</p>
<p>energygrps = Protein Non-Protein </p>
<p>; Pressure coupling is not on</p>
<p>Pcoupl = parrinello-rahman</p>
<p>tau_p = 0.5</p>
<p>compressibility = 4.5e-5</p>
<p>ref_p = 1.0</p></span><br></div>
<div class="gmail_quote">On Sat, Mar 7, 2009 at 4:33 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>jayant james wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi!
<div class="im"><br>I have appended the NMR structure to a part of the protein that was not resolved to the protein and now I want to perform simulated annealing of the 40 amino acids (NMR structure had 33 amino acids and to link I needed another 7 aa) that have been thrown into the crystal structure. I am new to this simulated annealing procedure. So please help me out as how to write out a typical pr.mdp file. I am thinking of increasing the temp of the appended piece protein piece to about 10000K (while the rest of the protein, solvent, Na+ and Cl- are at 300K) and slowly bring the temperature down to 300K, say, in about 100 ps and then continue to perform MD simulations.<br>
</div></blockquote><br>Running a protein segment at 10000 K with solvent at 300 K will probably lead to some wild behavior of that protein segment, clashes with the solvent, and possibly an explosion of your system. Just thinking ahead...
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">1) So would it be the wise time to apply distance constraints from the protein at 300K to the appended peptide while performing simulated annealing?<br>
</blockquote><br></div>If you have actual NMR data, perhaps. But attempting to simulate at 10000 K while simultaneously applying distance restraints might be a difficult task (consider a lower temperature).
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">2) If so what would be a good temperature to set it to kick in? I am really confused as to how I am going to specify these 40 residues to be the group that needs to be heated up.<br>
</blockquote><br></div>Warm it up from some low temperature. There is an example at:<br><br><a href="http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa" target="_blank">http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa</a><br>
<br>If you want a separate temperature coupling group, make a special index group for it. No idea if that will actually work, but that's how you treat components of your system differently, in general.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">3) Usually I have tc-grps specified in pr.mdp as Protein and Non-Protein. So how would I go about setting up the temperature groups during the simulated annealing protocol?<br>
</blockquote><br></div>With the special index group. See #2.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks<br>JJ
<div class="im"><br><br><br> On Thu, Feb 26, 2009 at 4:47 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> jayant james wrote:<br><br> Hi!<br> I have a question with regard to a system that I am attempting<br> to model.<br> The N-terminal of chain of the protein was not resolved<br> crystallographically but was later solved by NMR.<br>
Now my plan is to append the NMR structure on to chain A of the<br> protein and perform simulated annealing only for the appended<br> NMR fragment. To help it find it biologically relevent<br> orientation in the system I could also apply distance restraints<br>
that I have.<br> Is this possible in Gromacs?<br><br><br> All except that actual construction part (modeling the two segments<br> together), yes.<br><br> -Justin<br><br> thanks<br> JJ<br><br>
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<div class="im"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br></div>ICTAS Doctoral Scholar
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