From: Amr Zeinalabideen Majul (amajul_at_gmu.edu)
Date: Mon May 24 2010 - 14:48:47 CDT
I am working on simulating a certain membrane in a water box and had a few questions regarding boundary conditions.
1. The NAMD User guide says that periodic boundary conditions are provided in NAMD in 1, 2 or 3 dimensions. How would I simulate my my membrane in only the x and y direction? I haven't found any example of turning off the image cells in the z direction. Do I just write 0 0 0 for the z basis vector, or will that simply place the image cell on top of each other?
2. I read on the namd listings mention of creating a water slab. I searched for more detail, but there was no specific explanation of how to do this in NAMD. Is it possible to have a different image cell in the Z direction than the X-Y direction? For example, If my membrane is horizontal in the x,y plane, I want water on top and below it, not more membrane replicated.
Thanks in Advance,
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