[gmx-users] salt concentration

[Netaly Khazanov]

Indeed :)
Thank you for such detailed answer.

Have a great day!

On Tue, Nov 14, 2017 at 9:52 AM, Alex <nedomacho at gmail.com> wrote:

> 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
>>>>> D-85748 Garching
>>>>> Tel: +49 8928915730
>>>>> Fax: +49 8928915714
>>>>>
>>>>> Email: j.hermann at lrz.tum.de
>>>>> http://www.biovt.mw.tum.de/
>>>>>
>>>>> --
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>>>>
>>>>
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-- 
Netaly