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
molecules.
> 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
simulation.
> 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: 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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Received on Thu Nov 23 2000 - 15:48:04 PST
