VMD-L Mailing List

From: Robert Brunner (rbrunner_at_illinois.edu)
Date: Tue Mar 01 2011 - 14:15:25 CST

On Mar 1, 2011, at 11:30 AM, Mao Mao wrote:

> Hi all,
>
> I am a new user of VMD. I am trying to build a inorganic channel using the Inorganic builder. Basically I created a cuboid and added a cylinder block in the z-axis direction. Then I used "add bonds" and "solvate". I was just wondering if I am doing the right thing.
> Another question is about the "Find surface atoms" task. In the documentation I found "A grid is placed over the volume of the periodic cell, and each grid point is considered a vacuum grid point if no atoms fall within a sphere (bubble) of radius r centered on that grid point." My question is what is the periodic cell? If a grid is placed over the entire volume ( eg. read in .psf and .pdb files), wouldn't that make every atom a shell atom? I just need help understanding how it works.
> Any help will be appreciated.
>
> Mao

The Inorganic builder's bond building is purely geometrical. For crystalline materials it probably will do a fairly good job if you know the characteristic bond lengths in your material, but for amorphous materials you need to consider how you want to define the bonds.

For periodic structures, the grid takes the periodic images into account, and uses the periodic box originally defined when laying out the uncut block of material. So, atoms near the edge of the periodic box will see particles in the periodic image.

Consider the 2D version of a structure here. dots and 'X's represent the unoccupied and occupied grid points. Ignore atoms for the moment.

........
........
........
XXX..XXX
XXX..XXX
XXX..XXX
........
........
........

The surface atoms would be the 'O's here. (ignore the fact that the atoms just happen to line up with the grid above).

--------
--------
--------
OOO--OOO
--O--O--
OOO--OOO
--------
--------
--------

Because the atoms at the left and right sides of the structure see only 'X's in the occupancy grid and its periodic images.

Does that clarify?

Robert

----------------------------------------------
Robert Brunner
rbrunner_at_illinois.edu
217-333-7677