[gmx-users] salt concentration

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Mon Nov 13 13:37:07 CET 2017

Hi Netaly,

one way would be to calculate the number of Na, Cl, and Mg ions by hand, 
i.e. with the box size and the respective concentrations, and add the 
correct amount of ions in two steps, with the flags -np or -nn. E.g. in 
the first step you add Na and Cl and in the second you add Mg.

All the best


On 13.11.2017 13:31, Netaly Khazanov wrote:
> Dear Gromacs User,
> Is it possible to simulate system with two salt concentrations , e.g. NaCl
> 0.1 mol/L and MgCl2 0.002 mol/liter?
> The commands that i am using you can see below:
> grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr
> genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA -
> nname CL -neutral -conc 0.1
> grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr
> genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top -pname
> MG -pq 2 -nname CL -neutral -conc 0.002
> The message that I got after the execution of the last command is :"No ions
> to add and no potential to calculate."
> Is it right way to do it?
> Thank you in advance.
> Netaly

*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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D-85748 Garching
Tel: +49 8928915730
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Email: j.hermann at lrz.tum.de

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