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

Berk Hess hess at kth.se
Thu Feb 11 15:38:32 CET 2021


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



On 2/11/21 3:29 PM, Lorién López Villellas 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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