Hi,
I would like to know your opinions about the dielectric constant for MD.
For MD in vacuum, I think people often use distance dependent dielectric
constant, such as e=2r or e=4r. If MD is fully solvated, we use e=1, I
think this is common sense (Maybe not).
In my simulation, I would like to partially solvate only a part of large
protein, and put CAP to fix water molecules. For example, for a protein of
100x100x100 Angstrom size, I solvate around catalitic site by water sphere
of radius=25 Angstrom.
Which dielectric constant is appropriate for this case, do you think? Of
course it will depend on parameter set. I'm interested in AMBER94 parameter
set.
Thanks,
Osamu Miyashita
UCSD Physics
Received on Wed Jul 31 2002 - 11:55:58 PDT
