[gmx-users] salt concentration

[Netaly Khazanov]

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.Hermann at 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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-- 
Netaly