[gmx-users] Ion concentration of genion vs charmm-gui

[Ali Khan]

Sorry Mark,

I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232 potassium
atoms. Its a small difference, and both methods have the same box size.


On Tue, May 13, 2014 at 3:38 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Sounds like a problem for a high-school chemistry test ;-) concentration =
> quantity / volume. From the factor of ~1000, probably you're inputting box
> sizes in A instead of nm, or vice-versa, somewhere.
>
> Mark
>
>
> On Tue, May 13, 2014 at 8:43 PM, Ali Khan <akk5r at virginia.edu> wrote:
>
> > Hey,
> >
> > I generated a membrane in charmm-gui that I will be simulating in
> gromacs.
> > I am using genion to add 0.14 M potassium by using the -conc flag. In a
> box
> > with dimensions 13.5355 nm x 13.5355 nm x 13 nm, genion states that I
> > should add 201 K atoms. When I constructed the system in charmm-gui, the
> > server stated that I should add 232 potassium ions to reach a 0.14 M
> > concentration. Does anyone have a suggestion of which potassium ion
> number
> > I should go with?
> >
> > Best Wishes,
> > Ali Khan
> > --
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