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

[Antonio Baptista]

Actually, your target concentration usually refers to the macroscopic 
solution bulk, not to the simulation box. Therefore, it is generally more 
correct to think in terms of the ion:solvent molar ratios -- that is, turn 
your molar concentration into the corresponding macroscopic ion:solvent 
molar ratios, and then use those ratios in your box.

In many cases it doesn't make much difference which approach you use, 
because the fraction of box volume occupied by the non-solvent part of the 
simulated system is often very small. However, a membrane typically 
occupies a substantial volume of your box, so I would advise the molar 
fraction approach in your case.

(Strictly speaking, not even that is necessarily correct, because your 
system of interest may induce a local ion concentration different from the 
bulk one. But that is an entirely different issue.)

Best,
Antonio


On Tue, 13 May 2014, Mark Abraham 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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--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619         email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
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