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,