<div>Hi!</div>
<div>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. </div>
<div>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? </div>
<div>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. </div>
<div>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?</div>
<div>Thanks</div>
<div>JJ</div>
<div><br><br> </div>
<div class="gmail_quote">On Thu, Feb 26, 2009 at 4:47 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">
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<div class="h5"><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!<br>I have a question with regard to a system that I am attempting to model.<br>The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR.<br>
Now my plan is to append the NMR structure on to chain A of the protein and perform simulated annealing only for the appended NMR fragment. To help it find it biologically relevent orientation in the system I could also apply distance restraints that I have.<br>
Is this possible in Gromacs?<br></blockquote><br></div></div>All except that actual construction part (modeling the two segments together), yes.<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<br><br><br>------------------------------------------------------------------------<br><br>_______________________________________________<br>
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