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Re: [ESPResSo-users] Polymer between Lennard-Jones walls

From: Axel Arnold
Subject: Re: [ESPResSo-users] Polymer between Lennard-Jones walls
Date: Wed, 14 Nov 2012 18:45:19 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:16.0) Gecko/20121028 Thunderbird/16.0.2

On 11/14/2012 06:35 PM, Heng ZHANG wrote:

I am testing a polymer system between two Lennard Jones walls. I set up the constraint in the middle of the simulation box with pbc, but it always came back with the error message, 061 wall constraint 1 violated by particle.

The related codes are as follows:

setmd box_l         $box_length $box_length $box_length
setmd periodic         1 1 1
constraint wall normal 0 0 -1 dist [expr -0.5*$box_length] type 2
inter 0 2 lj-gen $lj_eps4 $lj_sig4 $lj_cut4 $lj_shift4 0 12 6 1 2
inter 1 2 lj-gen $lj_eps4 $lj_sig4 $lj_cut4 $lj_shift4 0 12 6 1 2
polymer $num_polymer $monomers_per_chain $bond_length mode RW bond 1 constraints

Do you have only one constraint? That can't work, particles will move out on the other side of the box, and reenter behind the first constraint, leading to the error. Also, physically it doesn't make sense to have only one one-sided wall in PBC. ESPResSo doesn't have two-sided walls, you need to add the second one.

Also, I am thinking whether the origin is at the corner of the simulation box, since from the blockfile of positions the center of the box is not there.

The box is from 0 to box_l in all directions, so your wall at the moment is in the center of the box, which is probably also not what you want.

On the other hand, I tried to simulate without pbc, adding two walls on top and bottom, but what is it to be done about x and y direction? I also used constraints in these two dimensions without LJ potential, but it does not work, by which I mean the x and y components of the particles are out of the box.
That I don't understand. Do you want periodic boundary conditions in x and y, or not? If not, then the system is open, and particles can diffuse far away in  x and y. If you don't want the system open, then you need to add walls.


JP Dr. Axel Arnold	     Tel: +49 711 685 67609
ICP, Universität Stuttgart   Email: address@hidden
Allmandring 3
70569 Stuttgart, Germany

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