[gmx-users] Polymer entanglement simulation

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 7 20:19:02 CET 2009

Tree wrote:
> Dear Users:
> Hello?
> As you might know, I am trying to simulate polymer chains with gromacs.
> Thanks to Justin's large help, I can build topology, which is the 
> essential to actually run the MD.
> After getting the MD result, I have a serious question.
> For polymer, as same as the other biopolymers, I assigned potential 
> parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values.
> I believe the grompp was working well, because there was no error 
> message at all.
> 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.
> That motion, I believe, should consist of bond, angle, dihedral, 
> improper, as we see in protein simulations.

Entanglement between chains?  That would be a result on nonbonded interactions 
between (or among) the chains.

> In this case, would you please explain what I have done wrong...?
> 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.

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.

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 

More than likely, this is a simple question of timeframe and appropriate 
sampling, which is the inherent limitation in any MD simulation.


> Please help me!
> (Hopefully I am becoming more prepared for a real polymer simulation guy...)
> Thank you!
> Sincerely,
> C Kim
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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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