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

Joe Jordan e.jjordan12 at gmail.com
Thu Feb 11 15:52:50 CET 2021

Hi Lorién,

Working with the legacy gromacs topology data structures, such as the
iatoms (really just a vector of ints) and iparams can be quite challenging.
Additionally, adding new code to constraints code is likely to face
challenges based on the core gromacs team being hesitant to take on new
maintenance burdens. However, depending on how much effort you have to
spend on this, I might suggest that you could check out the nblib topology
and force calculation API in gromacs 2021. Using this, it could be much
easier to implement your new algorithm. Please have a look at the sample
scripts in api/nblib/samples to get an idea of how, for instance, listed
forces such as bonds are handled by nblib. If this looks promising, perhaps
we can have a chat about potential integration pathways.


On Thu, Feb 11, 2021 at 3:30 PM Lorién López Villellas <lorien.lopez at bsc.es>

> 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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