AMBER Archive (2004)Subject: AMBER: one question about dielectric dependent model
From: Xiaowei (David) Li (xl3a_at_virginia.edu)
Date: Sun Dec 05 2004  11:42:56 CST
Dear AMBER users:
It is widely used technique to mimic the the influence of solvent using
implicit solvent(Generally, water). In AMBER, my understanding is that
there are two methods to use implicit solvent. One is GeneralizedBorn
(GB) model , and the other is to use distancedependent dielectric
model. Beause there is no GB model implemented in NMODE, so I use
distantcedependent dielectic model when I perform normal mode analysis
of nucleic acids. My question is concering about the distancedependent
model in AMBER.
Based on the DebyeHückel model, the screened Coulomb potential (phi) is
phi=(Z*q)/(epsilon *r) exp(kr), here the 1/k is the DH length, epsilon
is the dielectric constant in vacumm.
Therefore, the effective dielectric constant is (epsilon * exp(kr)). If
kr<1, then exp(kr) is approximated as (1+kr). So the effective
dielectric constant is (epsilon*(1+kr)).
In NMODE, we can set dielc=14 and idiel=0 to get the effective
dielectric constant as (14)*r, which means kr>>1 and the dielectric
constant is distant dependent. However, if the amount of water is very
small, then k is very close to 0. Thus, we should set the dielectric
constant as (epsilon*(1+kr)), instead of (epsilon*kr). But it seems to
me that there is no options in AMBER to set the dielectric constant as
(epsilon*(1+kr)). In other words, we can set constant dielectric or
distantdependent dielectric constant in AMBER. But there is
discontinuity between these two cases. This is my understanding about
this question. If I am wrong, please feel free to correct me. Thank you
very much.
Best,

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