Re: [AMBER] Algorithm Details of Addions/Addions2

From: David A Case <>
Date: Thu, 20 May 2021 09:15:17 -0400

On Mon, May 17, 2021, Robert Molt wrote:
>I am not clear on some of the specifics of how addions works.
>2.) One creates a grid and adds the ions in a "shell" around

I think addIons creates a 3-D grid around the solute; I'm not sure how big
it is. Then it computes the electrostatic potential at each point on the
grid and chooses the most favorable spot. My understanding(?) is that the
electrostatic potential is re-calculated after each ion is placed, and the
procedure is repeated until the requested number of ions is added.

Unless someone else on the list chimes in, you'll probably need to study the
code itself to get the real info.


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Received on Thu May 20 2021 - 06:30:02 PDT
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