Zhou Bo wrote:
Hi all,
I want to simulate a water/solid interface, like water on a HOPG
surface. I have some questions in construction of the system:
The system have a two-layer graphite surface (in the bottom of the box)
, a 3 nm thickness of water layer on it, and a vacuum region on the water.
Questions:
1) I have to freeze the two-layer graphite surface, NVT ensemble
is better to use than NPT. Am I right?
yes, also because of the vacuum.
2) Should I remove the com motion when I put a protein into the
water, because of the frozen groups ?
remove com only for the other groups.
3) I set the minimal distance between the graphite and the edge of
box to 0.5 nm (half of the cutoff), but I found some water slipped out
of the interface just from the box edge. Does anyone have suggestions to
do such a system? I think if I set the distance less than 0.5nm, the
water maybe not slip out. Although the interface will interact with
itself for the unreasonable distance, it does not matter because it is
just a frozen group. May it is a stupid idea.
don't understand the question.
Thank you
Bo Zhou
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