[gmx-users] Polymer entanglement simulation

[Tree]

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

>
>
> Mark Abraham wrote:
>
>> ----- Original Message -----
>> From: Tree <tree.csc at gmail.com>
>> Date: Sunday, March 8, 2009 6:35
>> Subject: Re: [gmx-users] Polymer entanglement simulation
>> To: jalemkul at vt.edu, Discussion list for GROMACS users <
>> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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