AMBER Archive (2001)

Subject: Delphi Calculations

From: Guanglei Cui (cuigl_at_ilion.bio.sunysb.edu)
Date: Tue Apr 10 2001 - 14:15:01 CDT

Dear AMBER users,
    I'm sorry for asking an unrelated question. I'm trying to calculate the
solvation energy of a small protein, which has a size of 30A x 30A x 30A. I
set the box fill to be 50%. However, I couldn't use scale, the grid
resolution, to 4 grids/A, even though the resulted number of grids is
roughly 240, less than the maximum 257 defined in the code. It gives me Bus
Error. I had to fall back and reduce the scale to 3 grids/A. I even tried to
recompile delphi with a larger ngrid, it still didn't work. I wonder if I
did anything improperly or there is a way to around this. Memory size isn't
a problem for me. I want to compare different comformations, therefore
accurate energy is important for me. Using scale 2 gives an energy which
differs from scale=3 by 3kcal/mol. Thanks in advance.

Regards,

Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790