[gmx-developers] How to obtain the element of an atom?

[Lorién López Villellas]

Hi.

Why is the element number relevant for constraints? The element number is
> never used in MD calculations.


We have performed a heavy code optimization based on the structural
patterns of the peptide chains. In order to apply this optimization, we
need a very specific bond numbering. To get to this bond numbering, we use
a bond reordering phase. The reordering algorithm needs to know the
elements of the molecule's atoms to locate itself.

Working with the legacy gromacs topology data structures, such as the
> iatoms (really just a vector of ints) and iparams can be quite challenging.
> Additionally, adding new code to constraints code is likely to face
> challenges based on the core gromacs team being hesitant to take on new
> maintenance burdens. However, depending on how much effort you have to
> spend on this, I might suggest that you could check out the nblib topology
> and force calculation API in gromacs 2021. Using this, it could be much
> easier to implement your new algorithm. Please have a look at the sample
> scripts in api/nblib/samples to get an idea of how, for instance, listed
> forces such as bonds are handled by nblib. If this looks promising, perhaps
> we can have a chat about potential integration pathways.


This project has been running for some years now (since 2013), so we
started working with the old C-GROMACS data structures. So far, we have
used a custom benchmark, but now we want to evaluate our algorithm's
performance in a real environment. I will take a look at nblib.

Regards,
Lorién

El jue, 11 feb 2021 a las 15:52, Joe Jordan (<e.jjordan12 at gmail.com>)
escribió:

> Hi Lorién,
>
> Working with the legacy gromacs topology data structures, such as the
> iatoms (really just a vector of ints) and iparams can be quite challenging.
> Additionally, adding new code to constraints code is likely to face
> challenges based on the core gromacs team being hesitant to take on new
> maintenance burdens. However, depending on how much effort you have to
> spend on this, I might suggest that you could check out the nblib topology
> and force calculation API in gromacs 2021. Using this, it could be much
> easier to implement your new algorithm. Please have a look at the sample
> scripts in api/nblib/samples to get an idea of how, for instance, listed
> forces such as bonds are handled by nblib. If this looks promising, perhaps
> we can have a chat about potential integration pathways.
>
> Joe
>
> On Thu, Feb 11, 2021 at 3:30 PM Lorién López Villellas <
> lorien.lopez at bsc.es> wrote:
>
>> Hi all.
>>
>> We are working on a new parallel algorithm for imposing constraints based
>> on SHAKE. We are currently trying to integrate it into GROMACS.
>>
>> We use the iatoms array (topology of triplets of constraint type, and
>> indices of the two atoms that compose a bond) just like SHAKE. We need a
>> way to obtain the element (Carbon, Nitrogen, Hidrogen...) of each of the
>> atom indexes in iatoms. As far as we have researched, there is no way to
>> access that data from src/gromacs/mdlib/constr. Where is that information
>> stored?
>>
>> If there is no way to obtain an atom element, we could also adapt our
>> code to work with similar information if it exists.
>>
>> We really appreciate any help you can provide.
>> --
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