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

[Erik Marklund]

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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