Re: AMBER: General Questions

From: David A. Case <>
Date: Wed, 3 Mar 2004 05:22:14 -0800

On Tue, Mar 02, 2004, Sekwan Oh wrote:

> Suppose we have the system of the cubic box where the biomolecule is
> adsorbed on the in organic surface and where the solvent with ions are
> present.
> 1. Can we know Electrostatic Potential distribution throughout the system
> using GB implicit method?

Not without writing your own code.

> 2. Can we specify the type of salt ion in solvent (monovalent/divalent)?


> 3. Can we know the ion concentrations in the system?

You can set the desired ionic strength.

> 4. Can we set this box as a periodic boundary condition using implicit
> solvent method (GB)?


> 5. In order to get the force data of each atom, should we modify the code
> to obtain the data?


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Received on Wed Mar 03 2004 - 13:53:00 PST
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