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

[David van der Spoel]

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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> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se