<br><br><div class="gmail_quote">On Tue, Jan 10, 2012 at 7:07 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
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<br>
On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a> <mailto:<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>><u></u>> wrote:<br>
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<br>
<br>
On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Steven Neumann wrote:<br>
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Dear Gmx Users,<br>
My system includes: ions, water, two tubes made of carbon<br>
atoms, protein.<br>
I would like to run NVT (and then NPT) with position<br>
restarined dynamics of my protein and tubes.<br>
I am wondering whether this approach is good (two coupling<br>
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<br>
set tc_grps when I want to add ligand?<br>
<br>
<br>
I don't know a definitive answer here, so I'll throw out some<br>
ideas and hopefully stimulate some discussion. I create tc_grps<br>
based on species whose dynamics are intimately linked. For<br>
solvent, that includes water and ions. Are your protein and<br>
tube physically associated? <br>
<br>
They are not physically associated but I put my protein as close as<br>
possible to the tube and I want to run position restrained dynamics<br>
of my tube and first 4 residues of my protein (stimulating attached<br>
protein to my tube).<br>
<br>
<br>
Will you suggest attaching my protein directly to my tube in this case?<br>
<br>
<br>
</div></div></blockquote>
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I'm assuming by "attaching" you mean coupling in the same tc_grp? I wouldn't. This is a complex case (and again, I don't know a true answer here) - your system has the potential to be highly dynamic. Say the protein and tube bind, in which case they would (in theory) be coupled together. Say they never bind, and then if you couple them together they shouldn't be. You don't know a priori which way it will go.<div class="im">
<br></div></blockquote><div><br>No. I mean physically attached. That is why my first 4 resiudes are closed to the tube and position restrained. The best would be to attach it physically by sharing one atom. No clue how. My tube is a representation of the rest of the protein assembly (I am interested in the influence of charged "residues" represented by ions and non charged by carbon atoms within my tube - position restrained dynamics the tube) on my protein. What is more there is another tube above my protein (not attached) and I am interested also on the influence of those "residues" of the tube on my protein conformation. In future I want to do Umrella Sampling pulling my tube above to see free energy difference. <br>
<br></div><div> </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="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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If not, it doesn't make sense to me to couple them together. In<br>
reality, no group should ever be coupled independently, but<br>
limitations in thermostats make it necessary.<br>
<br>
<br>
Would you suggest specifing 3 groups in this case: Protein, Tube,<br>
Water_and_ions ?<br>
<br>
</blockquote>
<br></div>
Sounds about as good as any approach. It's where I'd start.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Regarding the ligand, where is it? Floating around in solvent,<br>
bound to the protein, or in the tube? The answer to that<br>
question motivates how you treat it.<br>
<br>
With this simulation there is no ligand. My next simulation will be<br>
with 10-20 ligands placed randomly around the protein. I want to<br>
assess the influence of lmy ligands to the stability of the protein,<br>
that is why I need a comparison (in water only and in water with<br>
ligands).<br>
I am wondering how to specify coupling groups in this case.<br>
<br>
</blockquote>
<br></div>
I would consider the ligands part of the solvent, because at such a high concentration, really what you're dealing with is almost a cosolvent situation. Another example of species that may mix differently, aggregate, deposit on different surfaces, etc. If there is existing literature on this topic (or even something peripherally related), try established protocols.<div class="HOEnZb">
<div class="h5"><br>
When I will add my ligands they will surely stack to the protein (maybe tube as well...) . No clue what will happen between
my protein and the tube above.<br></div></div></blockquote><div><br>Thank you,<br><br>Steven<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="HOEnZb"><div class="h5">
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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 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>
<br>
==============================<u></u>==========<br>
-- <br>
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