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
settings.
More than likely, this is a simple question of timeframe and appropriate
sampling, which is the inherent limitation in any MD simulation.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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