[AMBER] Algorithm Details of Addions/Addions2

From: Robert Molt <rwmolt07.gmail.com>
Date: Mon, 17 May 2021 12:12:37 -0400

Good afternoon,

I am not clear on some of the specifics of how addions works. Ignore the
fact that addions works around the solute and addions2 around both

1.) Is there a paper which mentions the specifics which I should cite?

2.) One creates a grid and adds the ions in a "shell" around
solutes/waters. By "shell," I believe the manual implies that one places
ions in a rough sphere around the solutes/waters? It then treats them as
point charges and minimizes the energy to arrive at a local minimum? I
assume solute/solvent are exactly zero charge. Are the ion point charges
free to move in all 3 dimensions? This would seem most expensive.

I am trying to write a paper using software-agnostic terms, as much as
possible. I would ideally like to say what I did, instead of the
keyword. However, I am realizing that I do not exactly understand how
this algorithm works.

Dr. Robert Molt Jr.
AMBER mailing list
Received on Mon May 17 2021 - 09:30:02 PDT
Custom Search