<br><br><div class="gmail_quote">On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote"><div class="im">On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div><br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
My system includes: ions, water, two tubes made of carbon atoms, protein.<br>
I would like to run NVT (and then NPT) with position restarined dynamics of my protein and tubes.<br>
I am wondering whether this approach is good (two coupling groups: Protein_Tubes and Water_and_ions??<br>
My thermostat in mdp file:<br>
Temperature coupling is on<br>
<br>
tcoupl = V-rescale ;<br>
<br>
tc_grps = Protein_Tubes Water_and_ions ; two coupling groups<br>
<br>
tau_t = 0.1 0.1 ; time constant<br>
<br>
ref_t = 298 298 ; reference temperature<br>
<br>
Please, let me know whether this apporach is ok. How can I set tc_grps when I want to add ligand?<br>
<br>
</blockquote>
<br></div></div>
I don't know a definitive answer here, so I'll throw out some ideas and hopefully stimulate some discussion. I create tc_grps based on species whose dynamics are intimately linked. For solvent, that includes water and ions. Are your protein and tube physically associated? </blockquote>
</div><div><br>They are not physically associated but I put my protein as close as possible to the tube and I want to run position restrained dynamics of my tube and first 4 residues of my protein (stimulating attached protein to my tube). <br>
</div></div></blockquote><div><br>Will you suggest attaching my protein directly to my tube in this case?<br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="gmail_quote"><div>
<br> <br></div><div class="im"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> If not, it doesn't make sense to me to couple them together. In reality, no group should ever be coupled independently, but limitations in thermostats make it necessary.<br>
</blockquote></div><div><br>Would you suggest specifing 3 groups in this case: Protein, Tube, Water_and_ions ? <br></div><div class="im"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Regarding the ligand, where is it? Floating around in solvent, bound to the protein, or in the tube? The answer to that question motivates how you treat it.<br>
<br></blockquote></div><div>With this simulation there is no ligand. My next simulation will be with 10-20 ligands placed randomly around the protein. I want to assess the influence of lmy ligands to the stability of the protein, that is why I need a comparison (in water only and in water with ligands). <br>
I am wondering how to specify coupling groups in this case.<span class="HOEnZb"><font color="#888888"><br><br>Steven <br> </font></span></div><div class="im"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
-Justin<br>
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<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" value="+15402319080" target="_blank">(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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