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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 03 2004 - 13:53:00 PST
