Just another word of caution... the following strategy:
addionsrand mol Cl- 0
addionsrand mol Na+ 2448 Cl- 2448
Also known as "add-then-neutralize" may fake the expected macroscopic salt concentration (see: https://doi.org/10.1021/acs.jctc.9b00953 for instance)
Best,
Matias
PS: you can apply "addionsrand" in one step by setting the corresponding amount of each ion ;-)
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Micholas D. Smith" <smithmd.ornl.gov>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 6 de Mayo 2020 14:18:27
Asunto: Re: [AMBER] [EXTERNAL] addions
Be careful adding 1M of any salt. Force-field parameters tend to have issues as you increase salt concentration.
(see: https://www.nature.com/articles/s41598-017-18633-y for instance)
-Micholas
-----Original Message-----
From: Jisha B <jisha.b.k0511.gmail.com>
Sent: Wednesday, May 6, 2020 11:55 AM
To: AMBER.ambermd.org
Subject: [EXTERNAL] [AMBER] addions
Dear all,
I have this system where I need to add the counterions of Na+ and the salt of 1M NaCl according to a protocol.
I am aware of how to add Na+ using "addions cc Na+ 0" command in tleap. But I have no idea how to add the salt part. How to do that? Could someone guide me on this? I am a beginner.
--
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Received on Wed May 06 2020 - 11:00:02 PDT
