[gmx-users] Polymer entanglement simulation

Tree tree.csc at gmail.com
Sat Mar 7 20:05:07 CET 2009

Dear Users:

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
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.

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.

Please help me!
(Hopefully I am becoming more prepared for a real polymer simulation guy...)

Thank you!


C Kim
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