[gmx-users] Polymer entanglement simulation

[Justin A. Lemkul]

Tree wrote:
> Dear Justin and Mark:
> 
> 
> Thank you for your reply.
> 
> Okay, regarding the 'entanglement' of a polymer, I can ask in a 
> different way, maybe.
> In a protein simulation, I've seen the motion of 'one' protein 
> macromolecule such as a sort of vibrating, folding, moving around, or 
> changing its shape (becoming thinner, thicker, spherical, or column, 
> etc...).

What you observe will also be highly dependent upon the protein itself.  Whereas 
a stable, well-folded protein may not do much over time, different proteins may 
be more dynamic (those that are intrinsically unstructured or unstable).

Just because a protein acts a certain way, does *not* mean that all simulation 
results will be comparable.  The choice of .mdp parameters will play a role as well.

> I understand that is originated from potentials defined as 'bond 
> (stretch)', 'angle', 'dihedrals' and 'improper dihedrals', which are 
> different from metal simulation.

Not entirely.  The force field functional form also includes nonbonded terms 
(L-J and Coulombic interactions) that will play a role in dynamics.  Hence why 
using cut-off for electrostatics is a bad choice, since you will get artefacts.

> So, my questions is whether "this understanding" is correct or not...
> If not, I hope to learn how those potentials work for the one 
> macromolecule.   
> 
> Since I can a result anyway, I thought it was okay... :)
> Right, I've changed the cutoff range with a artificial (and arbitrary) 
> guess...

The correct approach is to never be arbitrary.  Read the primary literature for 
that particular force field and how it was derived.  Read about how people use 
the force field and whether or not modifications to the original derivation are 
also accurate.

-Justin

> As suggested by Justin, I will change mdp file and increase the time 
> duration.
> If I get a good(?) result, I will post-!
> 
> Thank you so much.
> 
> 
> Sincerely yours,
> 
> Chansoo
> 
> On Sat, Mar 7, 2009 at 5:45 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Mark Abraham wrote:
> 
>         ----- Original Message -----
>         From: Tree <tree.csc at gmail.com <mailto:tree.csc at gmail.com>>
>         Date: Sunday, March 8, 2009 6:35
>         Subject: Re: [gmx-users] Polymer entanglement simulation
>         To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list
>         for GROMACS users <gmx-users at gromacs.org
>         <mailto: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 :-)
> 
> 
>     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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================