AMBER Archive (2004)

Subject: AMBER: Regarding Dielectric Constant in AMBER8

From: pande.vineet_at_fc.up.pt
Date: Thu Nov 25 2004 - 09:22:41 CST

Dear AMBER Users:

This question is about specifying the type of DIELECTRIC in Sander calculations.

When I use PBCs and PME, and specify dielc = 1.0, it refers to a constant
dielctric, which is reasonable in this case..

BUT, if I want to perform a minimization with a DISTANCE DEPENDENT DIELCTRIC, in
AMBER8 what shall I do? Because IDIEL flag no longer works in AMBER8. Is it that
if I specify dielc = 1.0, and do not use PBCs/PME, it would refer by default to
a "distance-dependent" and not a "constant"? And then how to switch on to
"constant" ,imagining that we are doing a stochastic simulation and we donīt
apply PBCs..

Thanks in advance!
Vineet Pande

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