[gmx-users] Non-periodic Boundary conditions

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 25 22:43:11 CET 2002

On Mon, 25 Mar 2002, Senthil Kandasamy wrote:

>How can I incorporate the wall into the picture ? I would have to
>incorporate some sort of a uniform repulsive potential at the position
>of the wall that would keep the water molecules from diffusing through
>I guess .
A simple way is to have two or three layers of water (say 0.6 nm) that are
position restrained acting as a wall. You'd have to check whether
something comes through ofcourse. 

If you want a physical wall, that would most easily be modeled by freezing
certain atoms. In the past we have also used long range disperion
corrections for a wall. (Wensink et al., Langmuir, don't know exact ref.)

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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