Re: [AMBER] MD simulation at 1M or 2M salt concentration

From: Jason Swails <>
Date: Mon, 29 Sep 2014 08:23:05 -0400

On Sun, 2014-09-28 at 09:59 +0800, 张后今 wrote:
> Hi, guys:
> I would like to do simulation with a halophilic enzyme. The optimal
> salt concentration for this protein is 2M salt. Is Amber suitable for
> this kind of work? I am not sure if the force fields have been tested
> at such high salt concentration.

This is more a question to ask about a specific set of ion parameters
within a force field, not of a piece of software. If you are simulating
monovalent salt ions, then the parameters should be pretty good. I
would suggest looking into the citations for the different ion
parameters provided within Amber and see what they say.

Divalent metal ions are a different story. I would recommend looking at
chapter 3, section 9 (page 45) in the Amber 14 manual for a more
thorough discussion of ion parameters (as well as a list of references
to consult for more information).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 29 2014 - 05:30:04 PDT
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