AMBER Archive (2003)

Subject: Re: AMBER: dielectric in sander

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 21 2003 - 10:52:57 CDT

On Mon, Jul 21, 2003, Michele Lunelli wrote:

> How can I in sander (amber 7) set a constant or
> distance-dependent dielectric constant, for a non
> periodic system (i.e. without using eedmeth=5)? Is it
> enough use the leap command 'set default dielectric'?
> Which is the default behavior in sander?

Constant dielectric is the default in sander; to get a distance-dependent
dielectric, you need to use the eedmeth=5 variable. These, along with
the "dielc" variable for sander are recommended (by me!) over the
set default dielectric command in LEaP.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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