[gmx-users] Polymer entanglement simulation
tree.csc at gmail.com
Sat Mar 7 20:34:46 CET 2009
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
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
In addition, I am putting my setting here.
==== Beginning ====
title = Poly
cpp = /lib/cpp
include = -I../top
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!
On Sat, Mar 7, 2009 at 2:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Tree wrote:
>> 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 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.
> Please help me!
>> (Hopefully I am becoming more prepared for a real polymer simulation
>> Thank you!
>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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