From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Wed Dec 17 2003 - 11:30:59 CST


if you are doing an md simulation you really don't want to do that.
only for poisson-boltzmann or other continuum type analysis should
you put in a dielectric by hand of say 80.0 for water and say 2.0 for

if you just want to do a standard md, use a value near 1.0 to 2.0
for the dielectric in the simulation. the fact that you are doing md
with the correct partial charges for water means that you
will get an 'effective' dielectric for the water filled regions near 80.

put a quicker answer is: you can't define different dielectrics
in different regions in NAMD (or at least i am pretty sure you can't).

write back if you want review type references for the use of
dielectric constants in different kinds of simulations.


On Wednesday, December 17, 2003, at 08:24 AM, Liu, Zhanwu wrote:

> Dear all,
> How can I use different dielectric constant in the simulation, for
> example,
> 80 for bulk water and 1.0 for lipid?
> Thanks
> Zhanwu
> ---------------------------
> Zhanwu Liu, Ph.D.
> University of Pittsburgh
> Department of Anesthesiology

Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143
tel: ++ 415.476.6585

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