You are right. I am simulating an infinetely thick box (i.e., infinetely thick in z direction), with free surfaces (non-periodic bcs) in x and y directions. Is there an alternate method I could try to equilibriate my system?
I see what you mean about the circular domain. I had thought of a similar idea earlier, but I was uncertain whether a fix, say like npt and non periodic bcs maintain the shape of the domain at all times? will the circular domain remain circular even after npt dynamics?
Thanks for your help,
Abilash.
You are right. I am simulating an infinetely thick box (i.e., infinetely
thick in z direction), with free surfaces (non-periodic bcs) in x and y
directions. Is there an alternate method I could try to equilibriate my
system?
well, in that case, more parts of your input don't make much sense.
why the enforce2d. that will kill all movement in z-direction.
please also note the implication of shrink wrap boundary conditions.
for a non-periodic system you have no real box volume.
I see what you mean about the circular domain. I had thought of a similar
idea earlier, but I was uncertain whether a fix, say like npt and non
periodic bcs maintain the shape of the domain at all times? will the
circular domain remain circular even after npt dynamics?
you could program some soft repulsive cylindrical wall potential
that will have particles return to the system if they stray too far.
but then again, one has to think carefully what value a simulation
has, where you enforce a shape that the system does not want to
stay in.
cheers,
axel.
Thanks axel for pointing that out.
please also note the implication of shrink wrap boundary conditions.
for a non-periodic system you have no real box volume.
why is that? I mean as long as we shrink wrap the system, can't we get a
meaningful volume out of the calculations? The "box" still covers all
the atoms in the system and only scales up (or down) depending on the
dynamics, right?
Abilash.
Quoting Axel Kohlmeyer <[email protected]>:
Thanks axel for pointing that out.
> please also note the implication of shrink wrap boundary conditions.
> for a non-periodic system you have no real box volume.
why is that? I mean as long as we shrink wrap the system, can't we get a
meaningful volume out of the calculations? The "box" still covers all
the atoms in the system and only scales up (or down) depending on the
dynamics, right?
yes, the z-dimension should have meaning, but the volume doesn't,
since - according to the documentation - with 's'-boundary the box
will be expanded as needed to accomodate all coordinates in x-,
and y-direction. i suspect this is where you get the volume
fluctuations from.
cheers,
axel.