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

From: Steve Plimpton <sjplimp@...24...>
Date: Mon, 26 Jun 2017 06:35:51 -0600

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
is blowing up, leading to bad dynamics.  Once you have a bad
force for a particular config, you should be able to debug
where it comes from.


On Sat, Jun 24, 2017 at 10:45 PM, Stefan Paquay <stefanpaquay@...24...> 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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