From: John Jumper (jumper_at_uchicago.edu)
Date: Fri Mar 30 2012 - 15:10:44 CDT
I am trying to run GBIS simulations with a SASA term, and the surface areas
calculated by NAMD 2.9b2 appear to be off by orders of magnitude. Trying to
trace the problem, I calculated the surface area using the alanin
configuration in the src directory. The configuration that I used is below,
and based on the scaling of the total energy with the surfaceTension
parameter, it appears that initial SASA of alanin.pdb is 1,000,000 A^2. This
is orders of magnitude greater than the true answer of about 1000 A^2.
In the configuration below I use a surface tension of 1.0 kcal/mol/A^2 to
make the problem obvious.
# This is a test namd configuration file
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