Random stopping of particles

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1

Hi,

I found that my simulation will randomly set the velocity of all of
the particles to zero, and then continue as usual (which is the only
explanation I can think of for the attached .gif) I thought that this
was because of an error when the particles escaped the bounding box,
but this time the simulation ran without claiming any particles were
lost. I have attached a gif i made using GIMP to show you what I mean.

animated.gif

2

Hi,

I found that my simulation will randomly set the velocity of all of
the particles to zero, and then continue as usual (which is the only

they are not randomly set to zero, but are apparently
adsorbed on the (green) slab. nothing mystical about it.

axel.

3

but if they're adsorbed then why do the floating particles stop? if
you look, there are three blue particles that are all on the top and
stop, and I find it odd that they would all adsorb at the exact same
time.

4

but if they're adsorbed then why do the floating particles stop? if

because they are adsorbed, too.
you forgot about periodic boundary conditions.
they are adsorbed to the _bottom_ of the green slab.

axel.

5

hmm, I turned off periodic boundary conditions and put walls around the whole thing, plus when I set the energy in the pairwise interactions (lj/cut) between the two particles to 0 I still have this freezing behavior.

I can attach the source code if you'd like. Also, shouldn't the rest of the polymer that isn't touching the base be moving as it was before the bottom adsorbed?

~Nickhil

6

hmm, I turned off periodic boundary conditions and put walls around the
whole thing, plus when I set the energy in the pairwise interactions
(lj/cut) between the two particles to 0 I still have this freezing behavior.

I can attach the source code if you'd like. Also, shouldn't the rest of the
polymer that isn't touching the base be moving as it was before the bottom
adsorbed?

i don't know. MD always does what you tell it to do and not
what you think it should do. i am confident that all the features
that you are using are working correctly, so whatever happens is
real. it mostly seems to be a matter of not being what you expect.

that is ultimately your problem. if you run across a clear cut
case where you can provide proof(!) that something is not
working correctly (i.e. as advertised in the documentation,
not what you would like it to do), then i would like to see
an input script for it. otherwise it would file as PEBCAC.

cheers,
   axel.