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

Berk Hess hess at kth.se
Wed Feb 17 08:58:42 CET 2021


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.



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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