[gmx-users] Polymer entanglement simulation

[Tree]

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.
This is also reason that I have suspected the topology file, which assign
force field...

In addition, I am putting my setting here.

==== Beginning ====
title                    = Poly
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 500000
nstxout                  = 5000
nstvout                  = 5000
nstlog                   = 5000
nstenergy                = 250
nstxtcout                = 250
xtc_groups = System
energygrps = System
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.7
coulombtype              = cut-off
rcoulomb                 = 0.9
rvdw                     = 0.8
tcoupl                   = Berendsen
tc-grps = carbon hydrogen
energygrps = carbon hydrogen
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
==== Ends ====

Thank you, always!


Sincerely,

C. Kim

On Sat, Mar 7, 2009 at 2:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>
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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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