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Re: [lammps-users] Semi-Flexible polymers in 2D

# Re: [lammps-users] Semi-Flexible polymers in 2D

 From: Stefan Paquay Date: Mon, 26 Jun 2017 15:39:38 -0400

Thanks for thinking with me Steve.

One of my colleagues remarked that potentially it could be due to the short bond length. This makes it possible for particles to overlap due to thermal fluctuations, especially if there's no steric repulsion between neighbours. Of course, if the particles are too close, their angle is not well-defined and they blow up. I'll run some analysis on this to see what the bond lengths are just before blowing up. Increasing the bond length seems to mitigate the issue so I'm thinking this might explain it just fine.

On Mon, Jun 26, 2017 at 10:13 AM, Steve Plimpton wrote:
also, another idea, you can use compute reduce
to print out the max force on any atom at each step.
If you do that every step, you might see a snapshot
or two where things go bad.  Then you can examine
the bad atoms on that step.

Steve

On Mon, Jun 26, 2017 at 6:35 AM, Steve Plimpton wrote:
I don't know any reason 2d would be different than 3d,
unless there is some sort of numerical instability in
the interactions you've specified, e.g. as angles go to 180.

You could print out forces every tilmestep and see if something
force for a particular config, you should be able to debug
where it comes from.

Steve

On Sat, Jun 24, 2017 at 10:45 PM, Stefan Paquay wrote:
Hi all,

I have noticed some not very intuitive behaviour when using a semi-flexible polymer (by means of harmonic bond and angle potentials) in a 2D simulation. See the attached input script.

I naively assumed that just subtracting out the force in the Z-direction will make this automagically work, because the angles can still relax in the 2D plane (and moreover, if the preferred angle is 180 degrees, everything should be fine).

However, what I see is that in the 2D simulation the polymer dynamics become unstable and the particles are all over the place. The same settings in 3D lead to a perfectly well-behaved situation. Disabling the angular potential removes the instability but, obviously, also doesn't lead to a semi-flexible polymer. Using a planar constraint from USER-MANIFOLD leads to the same issue (not surprisingly).

Therefore my question: Are there some caveats with regards to angle potentials and 2D simulations that I'm not aware of? Maybe it is related to the impossibility of constraining angles at 180 degrees with SHAKE? Is there any way in which this can work?

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