<div dir="ltr">Hi Lorién,<div><br></div><div>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.</div><div><br></div><div>Joe</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 11, 2021 at 3:30 PM Lorién López Villellas <<a href="mailto:lorien.lopez@bsc.es">lorien.lopez@bsc.es</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi all.<br><br>We are working on a new parallel algorithm for imposing constraints based on SHAKE. We are currently trying to integrate it into GROMACS.<br><br>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?<br><br>If there is no way to obtain an atom element, we could also adapt our code to work with similar information if it exists.<br><br>We really appreciate any help you can provide. <br></div>
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