VMD-L Mailing List

From: Mao Mao (maoyanren_at_gmail.com)
Date: Tue Mar 01 2011 - 11:30:53 CST

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