Bug in SASA for alanin example

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.

Thank you,


# This is a test namd configuration file

timestep 0.5
numsteps 1
structure alanin.psf
parameters alanin.params
coordinates alanin.pdb
exclude scaled1-4
1-4scaling 0.4
outputname output
margin 1.0
stepspercycle 3
temperature 0

switching on
switchdist 30.0
cutoff 30.0
pairlistdist 40.0

dcdfile alanin.dcd
dcdfreq 1

#restartname alanin.restart
#restartfreq 10

#langevin on
#langevinTemp 300.0
#langevincol O

#constraints on

#fma on

#seed 791064881
surfaceTension 1.00

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