Polymer simulation breaks


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Thanks a lot for your reply. As the initial configuration, I am using a
polymer which I generated it to be confined in a box,
with a fixed density, and so since I am using fixed boundaries, I was
assuming this will be a confined polymer. Am I wrong?

you are indeed wrong. there is no confinement potential
or equivalent to keep atoms from leaving the box.
you have to use one of the fix wall styles to add that.

fixed boundaries simply means, that they don't change
(like shrink-wrap boundaries).

Should I imply the confinement in another way. The initial configuration
file comes in the following:

Also, I assumed a harmonic bond style for the polymer atoms through the
following commands,
why is that you mention there is no bonded interaction in my system?
bond_style harmonic
bond_coeff 1 1.5 1.0

i didn't say that. i only noted, that your non-bonded
interactions are purely reflective, since you set the
cutoff to the minimum of the 12-6 lennard jones potential.
because of that, your molecules will *have* to leave
the box sooner or later without any other potential
pulling or pushing them back.