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

Thu May 15 18:02:01 CEST 2014

On 5/14/14, 1:15 PM, Ali Khan wrote:
> I just did. It turns out that when there is a charged lipid in the system
> (as in my case), charmm-gui increases the effective concentration to
> compensate for the system's net charge. I have pasted my discourse with
> them below.
>

If this is the case, I would expect genion to do the same thing, but you need to 
specify the behavior manually.  Did you use the -neutral flag when running 
genion, or did you just specify -conc?  The combination of -neutral and -conc 
0.14 should have given the same number of excess ions.  201 is the number of 
ions expected for a box of that size that is already neutral.

-Justin

> My email:
> I have a question. I generated a membrane using the charmm-gui membrane
> builder. The server generated a 2POPC:1POPS bilayer in a box with water.
> The box dimensions were 135.355 A x 135.355 A x 130 A. I asked membrane
> builder to added 140 mM KCl, and it recommended 232 positive ions and 46
> negative ions. I also made this ion calculation by hand using the volume of
> the box, and my calculation gave me 201 positive ions for 0.14 M. If I
> calculated the concentration of ions based solely on the amount of water
> molecules in the box (54682 water molecules), I obtain 139 positive ions to
> make 0.14 M. I am trying to figure out where is the discrepancy is.
>
> Reply:
> The discrepancy arises from the net charge of the system since you have PS
> lipid types. So, your effective concentration should be higher to
> compensate such system net charge.
>
>
>
> On Wed, May 14, 2014 at 1:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/14/14, 12:06 PM, Ali Khan wrote:
>>
>>> 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.
>>>
>>>
>> Better yet, please report it to the CHARMM-GUI people.  If there's
>> something wrong, it needs to be fixed.  There is a very easy email form to
>> fill out to report issues.
>>
>> -Justin
>>
>>
>>
>>> 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
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================