[gmx-users] Re: are wall atoms virtual ?

Peter C. Lai pcl at uab.edu
Sat Nov 3 00:23:38 CET 2012

Wall atoms are virtual in the sense that they are just special Z-axis 
boundary conditions based on the integration of the LJ potential parameterized 
by the atom type, integraton model, and specified density of the "wall". The
particles don't physically exist so you will not see them in VMD (because 
they are just a modification to the simulation box itself and don't show 
up in the coordinate file). I never got around to scripting pbctools to 
dynamically update the box outlines frame by frame either, but there is
probably a way to do that. Theoretically, your walls would be seen where the
lines are showing the top and bottom of the box :)

On 2012-11-01 10:37:43AM -0700, harshaljain950 wrote:
> I have defined the wall by adding nwall option in my mdp file, I didn't
> name it as 'carbon wall'. I just use this name to refer to this wall in
> discussions
> Do you have any documentation or tutorial regarding implementation of
> walls, I am in a great need of one as i am new to gromacs
> Thank you for replying
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics Div. of Research	| 705 South 20th Street
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