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

[Ali Khan]

By hand it is about 201 molecules. It is strange that the membrane builder
in charmm-gui gives a different answer for the same box dimensions. I guess
those of us that use the charmm-gui membrane builder should keep this in
mind.


On Wed, May 14, 2014 at 11:14 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
> wrote:

> Hi Ali,
>
> And what would you expect in this case, based on the definition of
> concentration?
>
> Erik
>
> On 14 May 2014, at 04:11, Ali Khan <akk5r at virginia.edu> wrote:
>
> > 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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