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

Berk Hess hess at kth.se
Thu Feb 11 17:30:59 CET 2021

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?



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