AMBER Archive (2004)

Subject: Re: AMBER: charge problem in minimization

From: David A. Case (
Date: Thu Jul 08 2004 - 15:54:54 CDT

On Tue, Jul 06, 2004, yen li wrote:
> I have a problem in the minimization of a charged argenine dipeptide molecule (overall charge is +2 units). I am using AMBER7 and the distance dependent dielectric for the simulation. The input file is given as below
> ntr=0,dielc=4,cut=300,

Amber implements the "dielc=4" option by internally dividing all of the
charges by sqrt(dielc), which is 2 in this case. This can lead a misleading
output, perhaps. Try a run with dielc=1, to see what happens.


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