[gmx-users] Adding ions
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.
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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