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[ESPResSo-users] Polymer between Lennard-Jones walls

From: Heng ZHANG
Subject: [ESPResSo-users] Polymer between Lennard-Jones walls
Date: Wed, 14 Nov 2012 17:35:33 +0000


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

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.

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.

Thank you very much for your help,

Heng Zhang
Theory of Soft Condensed Matter
162 a, avenue de la faiencerie, BRB 0.05
Universite du Luxembourg
1511 Luxembourg

Tel. (+352) 46 66 44 6291

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