[gmx-users] ions

[Mark Abraham]

----- Original Message -----
From: tahereh tekieh <golesang80 at gmail.com>
Date: Monday, May 17, 2010 18:01
Subject: Re: [gmx-users] ions
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> using second invocation of genion replaces new ions with the older ones if the they have same amount of ions.

That doesn't sound all that likely. What pair of genion commands do you say does that?

Alternatively, use genion for A+B ions of type A, and then select B of them randomly to replace by the B ion with a text editor. (To see how those lines should look, do a separate test insertion of B with genion!) Then edit the output .gro and .top by hand to reflect the changes. You will need to make the ordering of molecules in the coordinate file match the [ molecules ] section by re-ordering the A and B ions to be contiguous chunks.

Mark

> On Mon, May 17, 2010 at 12:23 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> 

> 
> 
----- Original Message -----
> 
From: tahereh tekieh <golesang80 at gmail.com>
> 
Date: Monday, May 17, 2010 17:47
> 
Subject: [gmx-users] ions
> 
To: gmx-users at gromacs.org

> 
> 
> hi gromacs users
> 
> how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion.

> 

> Add one lot of ions with genion. Then add another lot of ions with a second invocation of genion.

> 
> 
Mark

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