[gmx-users] Polymer entanglement simulation

[Mark Abraham]

----- 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 :-)

Mark