[gmx-users] Magnetic field in GROMACS

[حبيبة علي]

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
>>>> --
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-- 
Habiba Ali,
Department of Chemistry,
University of Mosul-Iraq