Hi,
I have a simulation box of polymer at equilibrium. Then I used the command fix indent to push all atoms into a sphere (with keyword side in). But, I got somethings in the boudary that I'm not understand.You can see that in the image joined. For test, I changed boundary p p p ==> f f f but it's still like that.
Thanks for the discussion.
FixIndentSphere.bmp (900 KB)
Periodic boundaries or not should make no difference
so long as the sphere boundary is far from the box boundary.
The sphere boundary effectively becomes
the particle boundary.
Anytime you push on a stiff system you have to worry
about how hard you are pushing and how fast you are
trying to change it. Many systems will not respond well
unless you do it very gradually.
Steve
Periodic boundaries or not should make no difference
so long as the sphere boundary is far from the box boundary.
The sphere boundary effectively becomes
the particle boundary.Anytime you push on a stiff system you have to worry
about how hard you are pushing and how fast you are
trying to change it. Many systems will not respond well
unless you do it very gradually.
also, this will result in a very "ordered" system. question is, do you
want that? i might have tried the compression to a shape with a weak
soft core potential, so that the chains mix well and then gradually
unoverlap the atoms through raising the repulsive core. of course,
this will result in a rather disordered system. however, it may be
more realistic. but then again, this is just my guess.
axel.
