[gmx-users] Addition of ions in vacuum simulations

Thu Oct 18 09:04:59 CEST 2007

Hi Mark,

I think, it is not a chemistry question exactly. 
Genion command asks for a group whose atoms are replaced with ions.
I have no solvent molecules in my system. 
In this respect, how can I incorporate ions into my system? 



-----Original Message-----
From: "Mark Abraham" <mark.abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thu, 18 Oct 2007 16:49:15 +1000 (EST)
Subject: Re: [gmx-users] Addition of ions in vacuum simulations

> Hi all,
> I am simulating a charged peptide in vacuum. I want to neutralize my
> system by using genion command,and as expected it asks me a continuous
> solvent group for the replacement; however, I have no solvents.
> How can I add ions to my system if I am in vacuum? or Is it necessary to
> add ions while performing simulations in vacuum?

This is a chemistry question that will depend on your protein and what
you're trying to study. In some cases you might also consider modifying
the chemical groups so that there is not an ion there.


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