[gmx-users] Polymer entanglement simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 7 23:45:01 CET 2009

Mark Abraham wrote:
> ----- Original Message -----
> From: Tree <tree.csc at gmail.com>
> Date: Sunday, March 8, 2009 6:35
> Subject: Re: [gmx-users] Polymer entanglement simulation
> To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Dear Justin and Users:
>> Thank you for your fast reply.> 
>> First, I want to clarify the "entanglement", so I can get more accurate consult from you! :)
>> Of course, the non-bonded interaction makes entanglement "among" polymer chains.> 
>> However, "Entanglement" here means the "intra"chain (intramolecular) one.
>> 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.
> I don't understand what you mean by "entanglement", nor what this has to do with your force field parameters.
>> This is also reason that I have suspected the topology file, which assign force field...> 
>> In addition, I am putting my setting here.> 
>> tc-grps			 = carbon	hydrogen
> This is a train wreck waiting to happen. Please consider doing some more background reading and/or tutorial material :-)

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.

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.


> Mark
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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