AMBER Archive (2004)

Subject: AMBER: Dielectric Constant

From: Marsita M (
Date: Sat Dec 04 2004 - 05:42:36 CST

Dear all,

I have a confusion regarding the dielectric constant, after reading through
the archives and stuff on the internet, from what I understand ( please
correct me if im wrong), if lets say i want to roughly estimate the solvent
effects, i should be using distance-dependent dielectric constant (though it
wont be that correct) (if the simulation was carried out in vacuo), and in
amber, usually it is done by turning on eedmeth=5 in the &ewald list, and
use dielectric more than 1 (because dielc=1 is meant for vacum) , so there
are some suggestions to use dielc in the range of 2-4 coz it will performed
better (but I have no idea why, still need to do more reading on this) . am
i correct?

My first question is:

Is it okay to use dielectric=80 or will it introduce some instability to the

My second question is:

If I wanted to do a simulation in vacuo (ntb=0, igb=0), and I want to use
distance dependent dielectric instead of constant dielectric, so I should
turn on eedmeth=5, dielc=4 or 80 or other suggested values, and is it okay
to use cut=16? Or should I use larger value?

My third question is:

Which is better to use? constant dielectric (eedmeth=4) or distance
dependent dielectric(eedmeth=5) for simulation in vacuo? Because from what I
read, simulation using the distance dependent dielc could make the protein
to shrink as a result of the columbic interactions that are not properly

I am so confused, and I would appreciate it if somebody could give me some
hints or suggestions or corrections. And I would appreciate it very much if
any of you could suggest a few good reading materials on this area ( I have
read some but I need to read more, maybe there are some good articles that
im not aware of).

Thank you very much

Find det, du søger med MSN Søg

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to