Re: [AMBER] [EXTERNAL] addions

From: Matias Machado <>
Date: Wed, 06 May 2020 14:45:46 -0300 (UYT)

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: for instance)



PS: you can apply "addionsrand" in one step by setting the corresponding amount of each ion ;-)

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Micholas D. Smith" <>
Para: "AMBER Mailing List" <>
Enviados: MiƩrcoles, 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: for instance)


-----Original Message-----
From: Jisha B <>
Sent: Wednesday, May 6, 2020 11:55 AM
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
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