[gmx-users] gmx potential

[Shreyas Kaptan]

Hi.

Can anyone else try to answer my query about using gmx potential? I feel
there must be a way to use it to check the potential as applied by external
electric field.

Shreyas

On Thu, Mar 22, 2018 at 5:08 PM, Alex <nedomacho at gmail.com> wrote:

> Not sure what you mean by "correct." The "voltage" would be the field,
> times the box size in the direction of the field. Which is of course fake
> for a periodic boundary.
>
> If you're set on doing e.g. permeation studies that require applying a
> particular voltage across the box, external fields aren't really the way to
> go. Gromacs has a built-in computational electrophysiology (called CompEl,
> I think) protocol as part of the package. I've never used it, and it works
> by artificially maintaining an ionic concentration gradient, but it could
> be useful. The issue with zero actual correspondence between external
> fields and actual voltage drops isn't specific to Gromacs -- it's all part
> of Ewald sum legacy with electrostatics. I am only aware of one software
> suite that precisely solves Poisson on a real-space 3-D multigrid, but it's
> neither free, nor available to the public in any way.
>
> Alex
>
>
>
> On 3/22/2018 4:59 AM, Shreyas Kaptan wrote:
>
>> Okay. But then how can one confirm that the correct potential is applied
>> if
>> not by looking at the charge distribution?
>>
>> Shreyas
>>
>> On Thu, Mar 22, 2018, 00:32 Alex <nedomacho at gmail.com> wrote:
>>
>> No, you are exactly right -- it does NOT include the external field
>>> explicitly. The external field acts as a magical force here and gmx
>>> potential would produce a potential distribution based on the resulting
>>> charge distribution. The external field itself, once again, however, does
>>> not exist in that picture. I mean, you could add it as a linear drop of
>>> potential from one end to the other, but that is purely artificial. I
>>> stay
>>> away as much as possible from plotting charge distributions from
>>> simulations steered by external fields.
>>>
>>> Alex
>>>
>>> On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <shreyaskaptan at gmail.com
>>> >
>>> wrote:
>>>
>>> I am confused about which potential it actually calculates. As I
>>>> understand, the electric field (external) adds a force for each charged
>>>> particle. This ought to change the ion distribution. If I read the gmx
>>>> potential documentation right, it uses the distribution of the charges
>>>> in
>>>> the box to calculate the electrostatic potential in the box. Should that
>>>> not include the external field-induced potential? I admit, that I
>>>> assumed
>>>> that this was the dominant part of the potential.
>>>>
>>>> Was I wrong?
>>>>
>>>> Shreyas
>>>>
>>>> On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedomacho at gmail.com> wrote:
>>>>
>>>> It does exactly what it says it does. Which part is misunderstood?
>>>>>
>>>>> Alex
>>>>>
>>>>> On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <
>>>>>
>>>> shreyaskaptan at gmail.com
>>>
>>>> wrote:
>>>>>
>>>>> Hi.
>>>>>>
>>>>>> Thanks for the reply! Maybe I misunderstood the tool documentation.
>>>>>>
>>>>> So
>>>
>>>> what
>>>>>
>>>>>> does it *really* do?
>>>>>>
>>>>>> On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedomacho at gmail.com> wrote:
>>>>>>
>>>>>> Also, here is a message for the authors of the documentation:
>>>>>>>
>>>>>>> *-[no]spherical*(no)
>>>>>>>
>>>>>>>     Calculate spherical thingie
>>>>>>>
>>>>>>> Come on, guys. :)
>>>>>>>
>>>>>>> Alex
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 3/21/2018 1:24 PM, Alex wrote:
>>>>>>>
>>>>>>> Two things:
>>>>>>>>
>>>>>>>> 1. We cannot see your attachment, upload to a file share.
>>>>>>>>
>>>>>>>> 2. gmx potential does not reveal the actual potential drop due to
>>>>>>>> external electric field itself. What it does instead is described
>>>>>>>>
>>>>>>> in
>>>
>>>> the
>>>>>
>>>>>> utility documentation.
>>>>>>>>
>>>>>>>> Alex
>>>>>>>>
>>>>>>>>
>>>>>>>> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
>>>>>>>>
>>>>>>>> Dear GMX users,
>>>>>>>>>
>>>>>>>>> I am trying to use the gmx potential tool to calculate the
>>>>>>>>>
>>>>>>>> potential
>>>>
>>>>> created by applying a constant electric field in the Z-direction.
>>>>>>>>>
>>>>>>>>> I am using the 2018 gromacs version. The electric field was
>>>>>>>>>
>>>>>>>> applied
>>>
>>>> with:
>>>>>>
>>>>>>>
>>>>>>>>> electric-field-z         = 0.00625 0 0 0; 0.1 V voltage for 160
>>>>>>>>>
>>>>>>>> angstrom
>>>>>>
>>>>>>> Z
>>>>>>>>> len
>>>>>>>>>
>>>>>>>>> When I use the gmx potential (from 2016.1 version) on the result
>>>>>>>>>
>>>>>>>> of
>>>
>>>> the
>>>>>
>>>>>> simulation, I get the attached output.  I am not sure how to
>>>>>>>>>
>>>>>>>> interpret
>>>>>
>>>>>> the
>>>>>>>>> result. I expected a 100 V potential drop across the box, but I
>>>>>>>>>
>>>>>>>> do
>>>
>>>> not
>>>>>
>>>>>> s
>>>>>>
>>>>>>> that. Is that an error on part of my interpretation or is there
>>>>>>>>>
>>>>>>>> something
>>>>>>
>>>>>>> wrong with my setup?
>>>>>>>>>
>>>>>>>>> Thanks in advance!
>>>>>>>>>
>>>>>>>>> Shreyas
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
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>>>>>> or
>>>>
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Shreyas Sanjay Kaptan
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>
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>>>>>>
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>>>>
>>>> --
>>>> Shreyas Sanjay Kaptan
>>>> --
>>>> Gromacs Users mailing list
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-- 
Shreyas Sanjay Kaptan