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

[Berk Hess]

Hi,

Note that the order of atoms and constraints in mtop is only used in 
simulations without domain decomposition. With domain decomposition each 
domain has it's local and some non-local atoms and constraints. We will 
likely change the setup in mdrun soon such that atoms, interactions and 
constraints are also reordered without domain decomposition.

Cheers,

Berk

On 2/16/21 5:18 PM, Lorién López Villellas wrote:
> Hello again.
>
> As Dmitry suggested, we have been working with the /gmx_mtop_t/ data. 
> So far, it seems that it is what we needed.
>
> However, we are having some trouble with the /iatoms/ structure 
> (/idef->il[F_CONSTR].iatoms/ in 
> /Constraints::Impl::setConstraints()/). We are currently testing our 
> algorithm with the GROMACS-Lysozime tutorial (the md-simulation part). 
> The /elements_iatoms.txt/ file attached contains /iatoms/ and each 
> atom element when calling to setConstraints(). We see some weird bonds:
>
>   * Bond 1938, which is part of a cysteine amino acid (let us call it
>     amino acid x), connects atom 1910 (carbon) with atom 1913
>     (sulfur), forming a C-S bond, which is just right.
>   * Bond 100, connects atom 98 (sulfur) with atom 1913 (the sulfur
>     atom of amino acid x). As far as I know, a connection S-S is not
>     even possible in a peptide-chain.
>   * The bond that should connect atom 1913 with a hydrogen atom does
>     not exist.
>
> What is weird is that almost every bond makes sense, except some bonds 
> like the ones shown below. As this structure is used in SHAKE, I guess 
> we are doing something wrong.
>
> Thank you all in advance.
>
> Regards,
> Lorién
>
> El jue, 11 feb 2021 a las 19:16, Lorién López Villellas 
> (<lorien.lopez at bsc.es <mailto:lorien.lopez at bsc.es>>) escribió:
>
>     Hi.
>
>         One the possible solutions (there are atomic numbers stored in
>         the gmx_mtop_t)
>
>     I think we can work with that. Thanks!
>
>         But that would make the algorithm work only for proteins. Why
>         not do the numbering based on bond connectivity?
>
>
>     We have two versions of the algorithm, a sequential one that works
>     with any molecule and a parallel one that, as you say, only works
>     with proteins. The parallelization of the algorithm is based on
>     the structure of the peptide chain. The numbering we use is
>     extremely specific; each amino acid bond must always have the same
>     index. The reordering algorithm needs to identify each of the
>     molecule bonds precisely. We have not found a way to achieve that
>     without using the additional information that the atoms' element
>     provides.
>
>     Regards,
>     Lorién
>
>     El jue, 11 feb 2021 a las 17:30, Berk Hess (<hess at kth.se
>     <mailto:hess at kth.se>>) escribió:
>
>         On 2/11/21 4:22 PM, Lorién López Villellas wrote:
>>         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.
>>
>         But that would make the algorithm work only for proteins. Why
>         not do the numbering based on bond connectivity?
>
>         Cheers,
>
>         Berk
>
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