shear examples

Dear Axel,
Thanks for the explanation.
When I used the same commands for my case. energy increase sharply. In m y
opinion, there are atoms in mobile group being coincident with atoms in
boundary group
Could you please take a quick look attached script below.

without looking at the files,
if you want consistent behavior,
convert your restart to a data file.

i don't look at binary restart files
since they are not platform portable
and they make debugging a huge
pain, since you don't know what
has been defined inside the restart.


Sorry, I sent it again

input.poly.txt (1.14 KB)

data.file (4.46 MB)

i don't understand what this input is
supposed to be doing.

it looks completely messed up.
there appears to be some *really*
bad dynamics going on (if i write
out a trajectory it looks as if there
is a bullet piercing through a
glob of "worms").

i suggest you first set up a simple
calculation without any special
modifications or tricks. just to see
what is needed to equilibrate the
system (and that includes a proper
test without any thermostats to
check for energy conservation).

once you have this working, you
can introduce the "tricky stuff"
step by step.


Yes, the result is very bad. To be honest, I only want to mimic these commands in shear example for my case (polyethylene)
However, when I removed fix 3 boundary setforce 0.0 0.0 0.0. At moment the system is relaxed by using nve commonly.
The result looks not so bad. Energy is conserved (have just checked 10000 steps).

The purpose is that I want to relax the system with the frozen boundary before apply deformation.
Thanks so much.