It makes no difference whether you use -np/-nn or -conc. Your box is
simply too small to result in a nonzero ion count with something like
0.002 M. The check is rather simple: a cubic box has to be larger than
(1/n)^(1/3). For 0.002 M, that critical box size is 9.4 nm.
You can of course force any number of ions in there, but back-calculate
the corresponding concentration, given the box volume, and you'll see
that it's not what you want. This is exactly what GMX does when you call
-conc.
Alex
On 11/13/2017 11:54 PM, Netaly Khazanov wrote:
Thanks for your prompt replay.
I thougnt it would be more elegant way to do it using the commands.
If not that is what I am going to do.
Best,
Netaly
On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:
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
Johannes
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
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