VMD-L Mailing List

From: Patrick Redmill (patrick.s.redmill_at_Vanderbilt.Edu)
Date: Sat Apr 21 2007 - 10:14:19 CDT

Hi all,
   I have a troubling problem that I think some of you may be able to help
me with. I am using SASA to measure, well, the sasa of various caged
particles (like fullerenes). For open ended nanotubes, I want to pick
the size of my probe radius that will reflect the ability (or
inability) for a solvent to go inside the pore. In short, if it's a
thin tube, the probe shouldn't fit inside, if it's a fat one, it
should.

   My problem is that I don't see the expected changes in sasa when I
fiddle with my probe size. Intuitively, you'd think smaller probe size
= more solvent accesiblr area. However, when I choose srad = 1.4, I
get:

1742.80004883

Alternatively, when I chose srad = 2.2, I get:

1912.75878906

Obviously, my idea of what srad is, is incorrect, OR I'm setting up the
calculation wrong. For completeness, here are the commands I used to
execute the calculation.

set var [atomselect 0 "name C"]
$var set radius 1.95 (changing the atomic radii to suit my ff here)
measure sasa 1.4 $var

Thanks!

~Patrick