Mark Abraham wrote:
----- Original Message -----
From: Tree <[email protected]>
Date: Sunday, March 8, 2009 6:35
Subject: Re: [gmx-users] Polymer entanglement simulation
To: [email protected], Discussion list for GROMACS users <[email protected]>
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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