This is more of a scientific question than a technical one - I hope
this is the right place to ask.
I'm new to the CCP4 bundle. So far I've only used the AREAIMOL tool,
which determines the accessible surface area of a system. My system
is an irregular periodic slab and so I have used the following
options:
SMODE IMOL
TRANS
PROBE 0.75
OUTPUT
END
I have used such a small probe sphere radius because it's half of
the first peak in the radial distribution function, that is, more or
less half of the average first nearest-neighbor distance.
I'm doing this because my slab being amorphous I want to have a
systematic and unambiguous way of determining the number of surface
atoms. Using the settings above, AREAIMOL produces a number of
surface atoms in good agreement with a naive visual interpretation
of the structure, which feels right.
My question is if this is a sound approach and what alternative
criteria for computing the number of surface atoms are
available/used by the community.
Many thanks,
Miguel
-- Dr. Miguel Caro Postdoctoral researcher
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: [log in to unmask]
Work: [log in to unmask]
Website: http://mcaroba.dyndns.org