[gmx-users] salt concentration

[Alex]

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.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
>>>
>>>
>>>
>> --
>> ______________________________________
>> *Technische Universität München*
>> *Johannes Hermann, M.Sc.*
>> Lehrstuhl für Bioverf
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>>
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>>
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