Dear Justin and Users:<div><br></div><div><br></div><div>Thank you for your fast reply.</div><div><br></div><div>First, I want to clarify the "entanglement", so I can get more accurate consult from you! :)</div><div>
<br></div><div><div>Of course, the non-bonded interaction makes entanglement "among" polymer chains.</div></div><div><br></div><div>However, "Entanglement" here means the "intra"chain (intramolecular) one.</div>
<div>In other words, one chain polymer (having enough monomers inside, e.g. 1 chain polymer containing 20 monomers) can be entangled with itself. </div><div>This is the reason that I gave force filed parameters related to the bond (stretch), angle, dihedral, and improper dihedral.</div>
<div>This is also reason that I have suspected the topology file, which assign force field...</div><div><br></div><div>In addition, I am putting my setting here.</div><div><br></div><div>==== Beginning ====</div><div><div>
title = Poly</div><div>cpp = /lib/cpp</div><div>include = -I../top</div><div>define = </div><div>integrator = md</div><div>dt = 0.002</div>
<div>nsteps = 500000</div><div>nstxout = 5000</div><div>nstvout = 5000</div><div>nstlog = 5000</div><div>nstenergy = 250</div><div>nstxtcout = 250</div>
<div>xtc_groups<span class="Apple-tab-span" style="white-space:pre"> </span> = System</div><div>energygrps<span class="Apple-tab-span" style="white-space:pre"> </span> = System</div><div>nstlist = 10</div>
<div>ns_type = grid</div><div>rlist = 0.7</div><div>coulombtype = cut-off</div><div>rcoulomb = 0.9 </div><div>rvdw = 0.8</div><div>tcoupl = Berendsen</div>
<div>tc-grps<span class="Apple-tab-span" style="white-space:pre"> </span> = carbon<span class="Apple-tab-span" style="white-space:pre"> </span>hydrogen</div><div>energygrps<span class="Apple-tab-span" style="white-space:pre"> </span> = carbon<span class="Apple-tab-span" style="white-space:pre"> </span>hydrogen <span class="Apple-tab-span" style="white-space:pre"> </span></div>
<div>tau_t = 0.1 0.1</div><div>ref_t = 300 300</div><div>Pcoupl = Berendsen</div><div>tau_p = 1.0</div><div>compressibility = 4.5e-5</div>
<div>ref_p = 1.0</div><div>gen_vel = no</div><div>gen_temp = 300</div><div>gen_seed = 173529</div><div>constraints = all-bonds</div></div><div>
==== Ends ====</div><div><br></div><div>Thank you, always!</div><div><br></div><div><br></div><div>Sincerely,</div><div><br></div><div>C. Kim</div><div><br><div class="gmail_quote">On Sat, Mar 7, 2009 at 2:19 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>
Tree wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Users:<br>
<br>
<br>
Hello?<br>
As you might know, I am trying to simulate polymer chains with gromacs.<br>
Thanks to Justin's large help, I can build topology, which is the essential to actually run the MD.<br>
After getting the MD result, I have a serious question.<br>
<br>
For polymer, as same as the other biopolymers, I assigned potential parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values.<br>
I believe the grompp was working well, because there was no error message at all.<br>
After doing a set of actual simulations with my tpr file (and I've checked the processed topology file), unfortunately I could not see any "entanglement" motion.<br>
That motion, I believe, should consist of bond, angle, dihedral, improper, as we see in protein simulations.<br>
<br>
</blockquote>
<br></div>
Entanglement between chains? That would be a result on nonbonded interactions between (or among) the chains.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In this case, would you please explain what I have done wrong...?<br>
I guessed that the processed force filed (generated by "grompp") could be a problem, but according to Justin's explanations I think it is okay.<br>
<br>
</blockquote>
<br></div>
The "processed" topology is not generating a problem, per se. Whether or not the force field parameters you are using (i.e., those from OPLS-AA) are appropriate or not is what is the real question.<br>
<br>
How long are you simulating? It may be a question of timeframe. To equilibrate large polymers may take tens (if not hundreds) of nanoseconds. Another source of error could be the parameters you are specifying in your .mdp file. If you post that, we might be able to tell if there are any errors or inappropriate settings.<br>
<br>
More than likely, this is a simple question of timeframe and appropriate sampling, which is the inherent limitation in any MD simulation.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Please help me!<br>
(Hopefully I am becoming more prepared for a real polymer simulation guy...)<br>
<br>
Thank you!<br>
<br>
<br>
Sincerely,<br>
<br>
C Kim<br>
<br>
<br></div>
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-- <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>
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