AMBER Archive (2009)

Subject: Re: [AMBER] distance-dependent dielectric constant minimization

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Mon Nov 30 2009 - 23:31:58 CST

Dear Professor Case,

Thanks for your remind, I went back and read the manual again it just gives me a very brief introduce as" Dielectric multiplicative constant for the electrostatic interactions. Default is 1.0. Please note this is NOT related to dielectric constants for generalized Born simulations.". After read, I still do not know how to run the distance-dependent dielectric constant minimization. I ever read similar paper people did such minimization for some special purpose. But they never said how they did it.

Can you give me more detail? If it is on the tutorial and I missed again, I am really sorry for that!

Best wishes,

Rilei Yu

--- 09年11月30日，周一, case <case_at_biomaps.rutgers.edu> 写道：

发件人: case <case_at_biomaps.rutgers.edu>
主题: Re: [AMBER] distance-dependent dielectric constant minimization
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年11月30日,周一,下午9:02

On Mon, Nov 30, 2009, Rilei Yu wrote:
>
> I want to carry out distance-dependent dielectric constant minimization
> on my system. But I could not find similar operation in the tutorial,
> maybe I missed. Can anyone tell me how to carry out this step?
>
> Can I just add dielc=4r  in the min.in file for that?

For sander/pmemd, look at the "dielc" and "idiel" variables in the Users'
Manual.

For NAB, look at "dielc" and "diel".

...dac

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