Is there any way to 'shift' molecules from one part of simulation to another?

Sorry for the personal mail (it's just the default setting in pop3
client to avoid unnecessary spamming) and any insinuation regarding
your experience in MD! I dont think anyone here has doubt on that, I
was just covering my bases.

"c) the approach from the paper makes sense (finite system with extra
space), your approach doesn't."
How come is it different? idea is to measure force of the system in
equilibrium at different configuration (different separation
distance), what difference shall periodicity of sheets can cause on
MD? If i can maintain the pressure manually shall force felt on sheet
along z-direction be same in both cases?

Sorry for the personal mail (it's just the default setting in pop3
client to avoid unnecessary spamming) and any insinuation regarding
your experience in MD! I dont think anyone here has doubt on that, I
was just covering my bases.

"c) the approach from the paper makes sense (finite system with extra
space), your approach doesn't."
How come is it different? idea is to measure force of the system in
equilibrium at different configuration (different separation
distance), what difference shall periodicity of sheets can cause on
MD? If i can maintain the pressure manually shall force felt on sheet
along z-direction be same in both cases?

i have already explained the reason: in the method described in the
paper, the system is allowed to evolve by itself, while your approach
is making arbitrary changes. you are ignoring the fact that the force
you are measuring and the pressure that you are using as a guide to
adjust the system's configuration is directly correlated to the
property you are measuring.
the periodicity makes all the difference. that is my very point.

axel.

Thanks a lot for your patience and comments

" you are ignoring the fact that the force
you are measuring and the pressure that you are using as a guide to
adjust the system's configuration is directly correlated to the
property you are measuring."

I havent thought about this, neither am totally convinced, I will read
and work more to see what comes.
Thank you again for your time.