[gmx-users] salt concentration

[Alex]

I think that's high school stuff. :)

N -- number of ions.

V = a^3 -- volume (a is cube side length)

n -- concentration (1M = 6e+26 m-3, you have 0.002 M)

N = a^3*n > 1

a > (1/n)^(1/3).


On 11/14/2017 12:44 AM, Netaly Khazanov wrote:
> 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
>>>>>
>>>>>
>>>>>
>>>>> --
>>>> ______________________________________
>>>> *Technische Universität München*
>>>> *Johannes Hermann, M.Sc.*
>>>> Lehrstuhl für Bioverf
>>>> <https://maps.google.com/?q=uhl+f%C3%BCr+Bioverf&entry=gmail&source=g>
>>>> ahrenstechnik
>>>> Boltzmannstr. 15
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>>>> Tel: +49 8928915730
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>>>>
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>>>>
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>>>
>>>
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