Indeed :)
Thank you for such detailed answer.
Have a great day!
On Tue, Nov 14, 2017 at 9:52 AM, Alex 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
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 calcul
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 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 so
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
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.herm...@lrz.tu-muenchen.de> wrote:
> Hi Netaly,
>
> one way would be to calculate the number
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
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_NaC
