Dear Justin and Mark:<div><br></div><div><br></div><div>Thank you for your reply.</div><div><br></div><div>Okay, regarding the 'entanglement' of a polymer, I can ask in a different way, maybe.</div><div>In a protein simulation, I've seen the motion of 'one' protein macromolecule such as a sort of vibrating, folding, moving around, or changing its shape (becoming thinner, thicker, spherical, or column, etc...).</div>
<div>I understand that is originated from potentials defined as 'bond (stretch)', 'angle', 'dihedrals' and 'improper dihedrals', which are different from metal simulation.</div><div>So, my questions is whether "this understanding" is correct or not...</div>
<div>If not, I hope to learn how those potentials work for the one macromolecule. </div><div><br></div><div>Since I can a result anyway, I thought it was okay... :)</div><div>Right, I've changed the cutoff range with a artificial (and arbitrary) guess...</div>
<div>As suggested by Justin, I will change mdp file and increase the time duration.</div><div>If I get a good(?) result, I will post-!</div><div><br></div><div>Thank you so much.</div><div><br></div><div><br></div><div>Sincerely yours,</div>
<div><br></div><div>Chansoo</div><br><div class="gmail_quote">On Sat, Mar 7, 2009 at 5:45 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;">
<div class="im"><br>
<br>
Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
----- Original Message -----<br>
From: Tree <<a href="mailto:tree.csc@gmail.com" target="_blank">tree.csc@gmail.com</a>><br>
Date: Sunday, March 8, 2009 6:35<br>
Subject: Re: [gmx-users] Polymer entanglement simulation<br>
To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin and Users:<br>
<br>
Thank you for your fast reply.> First, I want to clarify the "entanglement", so I can get more accurate consult from you! :)<br>
<br>
Of course, the non-bonded interaction makes entanglement "among" polymer chains.> However, "Entanglement" here means the "intra"chain (intramolecular) one.<br>
In other words, one chain polymer (having enough monomers inside, e.g. 1 chain polymer containing 20 monomers) can be entangled with itself. > This is the reason that I gave force filed parameters related to the bond (stretch), angle, dihedral, and improper dihedral.<br>
</blockquote>
<br>
I don't understand what you mean by "entanglement", nor what this has to do with your force field parameters.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This is also reason that I have suspected the topology file, which assign force field...> In addition, I am putting my setting here.> <br>
</blockquote>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
tc-grps = carbon hydrogen<br>
</blockquote>
<br>
This is a train wreck waiting to happen. Please consider doing some more background reading and/or tutorial material :-)<br>
<br>
</blockquote>
<br></div>
As is using cut-off for electrostatics, with the bizarre cutoff's you've defined (rlist, rcoulomb, rvdw). Use PME with at least a 1.0-nm cutoff for all three and see if you get better results.<br>
<br>
Furthermore, as I said before, timeframe might be an issue. 1 ns is not nearly long enough to see such behavior. Try tens of nanoseconds, if not more.<br><font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark<br>
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<br></div><div class="im">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a 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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