Re: Question?

From: David Case <>
Date: Thu 23 Nov 2000 15:48:04 -0800

On Thu, Nov 23, 2000, Khatcharin Siriwong wrote:

> 1. What condition do you use generalized Born model (GB)? with or
> without solvent?

You would never use GB *with* explicit solvent; use GB if you want
to explore a relatively new approach to inluding aqueous solvation effects
without having an explicit description of each of the individual solvent

> 2. In Amber 6 manual, if IGB=3, it mean a calculation in vacuum (no
> solvent) with a distance-dependent dielectric. Is the GB and PME
> (particle-mesh Ewald) used in the case of IGB=3?

No: igb=3 is a "vacuum" simulation with just one change: the dielectric
constant is set to the distance in angstroms. It is not a periodic

> 3. How do you set the parameters if you want to run MD simulation with
> both the GB and PME?

This is not currently possible: you cannot run GB on a periodic system,
nor use PME with it. This comibination, although not impossible,
is unlikely to be implemented any time soon.

...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 Thu Nov 23 2000 - 15:48:04 PST
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