AMBER Archive (2003)

Subject: Re: AMBER: more questions about igb

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 20 2003 - 18:47:35 CDT

On Sun, Oct 19, 2003, Pingna Xu wrote:

>So does it mean that the
> distance-dependent dielectric model is different from the GB model?

yes.

> I I want to use the distance-dependent dielectric model, I should turn off the
> GB model by setting igb=0,right?

yes.

There are three separate variables:

ntb=0 means no periodicity; default is ntb=1, for perioidic

igb=0 means no generalized Born; this is the default

eedmeth=4 means constant dielectric; this is the default when ntb=0 and igb=0.
eedemth=5 means distance dependent dielectric; you have to specify this
explicity if you want it.

Note that the force fields you get when ntb=0 and igb=0 are not very
physcially realistic ones. This combination should only be used if you don't
need (or cannot afford) an accurate representation of the energies and forces
in the system.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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