>>>>> "Ilyas" == Ilyas Yildirim <yildirim.pas.rochester.edu> writes:
Ilyas> Another question is the following: When the bondii radii
Ilyas> for a specific type is set to zero, and igb=2 is used, I am
Ilyas> getting NaN results in the output file (when bondii radii
Ilyas> is not zero - even when it is very close to zero - the
Ilyas> result is ok). I was wondering why this is creating a
Ilyas> singularity in the system when implicit solvent is
Ilyas> used. Thanks in advance.
The standard formulae of GB theory include terms like 1/a_i, where a_i
is the radius of atom i, so I think a NaN is to be expected. As long
as atom i has any possiblity of being exposed to solvent, a radius of
zero is unphysical because the energy of moving a point charge from
one dielectric medium to another diverges to infinity in the limit of
a zero-sized point.
-Don
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Received on Wed Aug 02 2006 - 06:07:13 PDT
