[gmx-users] salt concentration

Netaly Khazanov netalyk at gmail.com
Mon Nov 13 13:32:12 CET 2017

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.


More information about the gromacs.org_gmx-users mailing list