AMBER Archive (2003)

Subject: AMBER: more questions about igb

From: Pingna Xu (px208_at_nyu.edu)
Date: Sun Oct 19 2003 - 22:54:49 CDT

I have read that paper. In the conclusion I found the sentence "Unlike distance-dependent dielectric models,it(GB model) includes both the screening of charge-charge interactions and..." So does it mean that the distance-dependent dielectric model is different from the GB model? If I want to use the distance-dependent dielectric model, I should turn off the GB model by setting igb=0,right? And in the tutorial based on amber 7,I found this sentence "Since sander assumes that the system is periodic, we need to turn off periodicity explicitly (NTB = 0) and also turn on the "implicit solvent" models, in this case a constant dielectric (which isn't an implicit solvent model) with IGB = 0". Now I am a little bit confused. I want to use a distance-dependent dielectric for my minimization. If I just Set ntb=0(no periodicity) and eedmeth=5, but say nothing about igb, do you think I can get a a distance-dependent dielectric? As you know,the default value of igb in amber is 0.Isn't it c
ontractive? Because setting ntb=0 and eedmeth=5 means a distance-dependent dielectric, while setting igb=0 means a constant dielectric... However, if I set igb>0, I turn on the GB model,which is different from distance-dependent dielectric models,according to that paper. So now it seems to me that once I set ntb=0 and eedmeth=5 to get a distance-dependent dielectric for my minimization, I can neither set igb=0 nor igb>0. Maybe I have misunderstood these sentences,resulting in getting this rediculous conclusion. Please help me out! Many thanks!

Pingna

----- Original Message -----
From: myang <myang_at_clarku.edu>
Date: Saturday, October 18, 2003 2:51 pm
Subject: RE: AMBER: one more question

> 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 [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
> meaningof 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,inwhich 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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