Re: AMBER: a question

From: David A. Case <>
Date: Fri, 17 Oct 2003 15:36:08 -0700

On Fri, Oct 17, 2003, Pingna Xu wrote:
> I have checked the website and found the sentence "Add the
> following note: in Amber 6, igb=3 was used to specify a distance-dependent
> dielectric; in Amber 7, this can be accomplished by setting eedmeth=5 in the
> &ewald namelist (see p. 100)." But I think my case is not an ewald one.So
> this sentence is not applicable to my case,right?I am not sure...

No,this is what you use, even thought you are not using Ewald. Set ntb=0
(no periodicity) and eedmeth=5 and you will get a distance-dependent
dielectric. Note that the manual does say (on p. 100) "[eedmeth=5] is
indended for non-periodic calculations, where no reciprocal term is computed".

...good luck..dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Oct 17 2003 - 23:53:00 PDT
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