AMBER Archive (2004)

Subject: AMBER: General Questions

From: Sekwan Oh (ohsk75_at_stanford.edu)
Date: Tue Mar 02 2004 - 18:07:08 CST

Dear Amber users,

I would like to ask you couple of questions.

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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?

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

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

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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I really appreciate your help. :)

Best wishes,

Sekwan

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