AMBER Archive (2002)

Subject: dielectric constant for partialy solvated MD

From: Miyashita, Osamu (omiyashita_at_ucsd.edu)
Date: Wed Jul 31 2002 - 13:55:58 CDT

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