[gmx-users] salt concentration

[Netaly Khazanov]

It makes sense.
I am not sure that I follow how you calculated the critical box size
depending on the the concentration.

On Tue, Nov 14, 2017 at 9:12 AM, Alex <nedomacho at gmail.com> wrote:

> 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
>>>>
>>>>
>>>>
>>>> --
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>>
>>
>>
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-- 
Netaly