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

From: Stefan Paquay <stefanpaquay@...24...>
Date: Sun, 25 Jun 2017 00:45:52 -0400

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?
units lj
dimension 2
boundary p p p

atom_style molecular

mass * 1.0

variable kbond   equal 12.5
variable kangle  equal 2.55
variable blength equal 0.25

bond_style harmonic
bond_coeff 1 ${kbond} ${blength}

angle_style harmonic
angle_coeff 1 ${kangle} 120

variable sigma equal 0.5
variable rc    equal "v_sigma * 2.0 ^ (1.0/6.0)"
pair_style lj/cut ${rc}
pair_coeff * * 1.0 ${sigma} ${rc}

pair_modify shift yes

timestep 0.0005
neighbor 6.0 bin
#neigh_modify exclude molecule/intra all

dump traj all custom 10000 chains.dump.bin id mol type x y z

velocity all create 1.0 412
fix twod all enforce2d
fix step all nve
thermo 100000
run 500000