[gmx-users] Adding ions

Justin Lemkul jalemkul at vt.edu
Sun Sep 10 20:43:05 CEST 2017

On 9/10/17 2:38 PM, Roshan Shrestha wrote:
>   For my system which has a net charge of -3, I wanted to add NaCl to a
> concentration of 0.1 M. So, I used *gmx genion -s ions.tpr -o 1aml_ions.gro
> -p topol.top -pname NA -nname CL -np 3 -conc 0.1 -neutral*
> I've got a feeling that to make my system neutral, I should be using only *gmx
> genion -s ions.tpr -o 1aml_ions.gro -p topol.top -pname NA -nname CL -conc
> 0.1 -neutral*
> So, is using the previous command incorrect ?
> Like, does -neutral in the command *gmx genion -s ions.tpr -o 1aml_ions.gro
> -p topol.top -pname NA -nname CL -np 3 -conc 0.1 -neutral *adds more ions,
> or it won't any since the system is already neutralized by adding 3
> positive Na ions.
How many ions were actually added in each case?  What does the topology 
say?  The use of -np and -conc should be mutually exclusive; I don't 
know which takes precedence in the code.  Using -np 3 *or* -neutral 
should accomplish the same thing - you will get 3 Na+ ions.  Using 
-neutral -conc 0.1 should give you excess ions, including the 3 Na+ 
needed to neutralize, which is what you want.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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