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

[Lorién López Villellas]

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>) 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
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.


http://bsc.es/disclaimer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20210211/858a9e44/attachment-0001.html>