AMBER Archive (2004)

Subject: AMBER: Dielectric Constant

From: Marsita M (marsitam_at_hotmail.com)
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
system?

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
shielded.

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

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