AMBER Archive (2003)

Subject: RE: AMBER: one more question

From: myang (myang_at_clarku.edu)
Date: Sat Oct 18 2003 - 13:51:33 CDT

The generalized Born solvation model means the solvent in your system is
implicit. You have no individual water molecules in your system. In amber
7, igb>0 is for GB model (implicit water). igb=0 is for explicit water
model. To get a better understanding of GB model, here is a good reference:
Gerneralized Born Models of Macromolecular Solvation Effects. Annu Rev.
Phys. Chem 2000,51:120-52. by Donald Bashford and David A. Case.

Hope this would help you out.

Best,
Ming

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]On Behalf Of
Pingna Xu
Sent: Saturday, October 18, 2003 2:02 PM
To: amber_at_scripps.edu
Subject: AMBER: one more question

Now I have one more question.You told me to set ntb=0 (no periodicity) and
eedmeth=5 and then I will get a distance-dependent dielectric.So does it
mean that I use the default igb,which is 0.I have noticed that the meaning
of igb in amber 7 is different from that in amber 6.I am really not sure
about the usage of the igb in amber 7.I have noticed the sentence "The
generalized Born solvation model can be used instead of explicit water for
non-polarizable force fields such as ff94 or ff99." Does it mean that the
generalized Born solvation model is generally the same as the explicit water
model?So now since I use the implicit water model,I should set igb=0,in
which no generalized born term is used,right?Thanks!

Yours,
Pingna

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Friday, October 17, 2003 6:36 pm
Subject: Re: AMBER: a question

> 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: 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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>

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