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On 11/14/2012 06:35 PM, Heng ZHANG
wrote:
Hello,
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.
Regards,
Axel
--
JP Dr. Axel Arnold Tel: +49 711 685 67609
ICP, Universität Stuttgart Email: address@hidden
Allmandring 3
70569 Stuttgart, Germany
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