[gmx-users] questions about simulation of water/solid interface

[Zhou Bo]

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?

2)       Should I remove the com motion when I put a protein into the water,
because of the frozen 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.

 

Thank you

 

Bo Zhou

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