AMBER Archive (2004)

Subject: Re: AMBER: General Questions

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 03 2004 - 07:22:14 CST

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)?

No.

>
> 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)?

NO.

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

Yes.

...dac
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