[gmx-users] Magnetic field in GROMACS

[حبيبة علي]

Dear Alex,

Thanks for your words. Yes, we have going on research and we look to the
future. But we are suffering from the lack of resources.

We did some work on electric field code but we could not call the velocity
of each particle to do the cross product with the magnetic field and also
our coding skills are horrible ;).

Thanks


On Thu, Jun 21, 2018 at 3:47 AM, Alex <nedomacho at gmail.com> wrote:

> I would at least first try to hardcode a test Lorentz force for e.g. a
> given constant magnetic field to see what happens and whether you can
> observe anything fun.
>
> On an unrelated note, I just want to say that it is great to see that
> there is scientific research going on in Iraq after years of war and
> destruction. Hats off to you and very best of luck!
>
> Alex
>
>
>
> On 6/21/2018 2:22 AM, حبيبة علي wrote:
>
>> I thought you are a developer ;)
>> I think updating electric field file is not a problem but the
>> complicated thing is what are the other files that related to it. Such as
>> how to implement it in mdp files which I think need to update different
>> files. If there are any analyzing commands need updating, etc
>> I  will keep trying
>> Thanks
>>
>>
>> On Thu, Jun 21, 2018 at 2:24 AM, Alex <nedomacho at gmail.com> wrote:
>>
>> Nah, I'm just a user. ;)
>>>
>>> What David and I were discussing is not a beginner's task (and I can't
>>> see
>>> a large number of users for that otherwise awesome functionality), but if
>>> you'd like to code the simple vector product, I am pretty sure there will
>>> be those who could direct you to the right files.
>>>
>>> Alex
>>>
>>>
>>>
>>> On 6/21/2018 1:08 AM, حبيبة علي wrote:
>>>
>>> Dear David and Alex,
>>>>
>>>> Thanks for the replies. I'm happy that you will consider it. You are the
>>>> developers and it is clear for you which file should be updated;
>>>>
>>>> Dear Ali,
>>>> My coding skills are very bad and I have no idea which file I need to
>>>> look
>>>> at.
>>>>
>>>> Best
>>>>
>>>> On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed <aa5635737 at gmail.com>
>>>> wrote:
>>>>
>>>> Hello,
>>>>
>>>>> I looked for that before and I tried updating the electric field code
>>>>> as
>>>>> both of them are related to Lorentz force. Unfortunately, I failed
>>>>> because
>>>>> there are different codes need to be updated.
>>>>> It would be amazing if the developers participate in this code.
>>>>> Thanks
>>>>> Ali
>>>>>
>>>>> On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel <
>>>>> spoel at xray.bmc.uu.se
>>>>> wrote:
>>>>>
>>>>> Den 2018-06-20 kl. 10:20, skrev Alex:
>>>>>
>>>>>> David,
>>>>>>
>>>>>>> I can think of many realistic cases when looking at the effects of
>>>>>>> magnetic fields in MD would be of interest, just not in what Gromacs
>>>>>>> is
>>>>>>> normally used for.
>>>>>>>
>>>>>>> It's just a completely different animal in terms of what causes those
>>>>>>> effects and Lorentz force applied to point charges would likely be a
>>>>>>>
>>>>>>> very
>>>>>> bad approximation. But in general, an implementation of
>>>>>> self-consistent
>>>>>>
>>>>>>> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing.
>>>>>>>
>>>>>>> Feel free to open a redmine issue to discuss it there.
>>>>>>>
>>>>>> We have an implementation of electric fields that can be used as a
>>>>>> template.
>>>>>>
>>>>>>
>>>>>> Alex
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Magnetic fields are typically very weak such that they are negligable
>>>>>>> in
>>>>>>>
>>>>>> realistic cases. This is why nobody bothered to implement it.
>>>>>>
>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>> http://www.icm.uu.se
>>>>>> --
>>>>>> Gromacs Users mailing list
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-- 
Habiba Ali,
Department of Chemistry,
University of Mosul-Iraq