Hi @Siam_Siraji
Ok – I missed that! If you think that the steps leading up to the failure are correct, the problem could be content versus parameters.
I’m also wondering if the job is simply running out of resources. This prior QA Tool error in protein-ligand md simulation in Gromacs failed for exceeding resources with “WARNING: This run will generate roughly 3843 Mb of data”. Your job is significantly larger with 13562 Mb of data.
The first warning (Note 1) indicates you could optimise the “Bond constraints (constraints)” setting to better fit your data. I’m not sure if changing that will address the second warning (Note 2) or not but you could try a test run. And, you could also try the advice from the other Q&A – lower the steps to check if a smaller job runs or not at the public site with the allocated resources.
Let’s also pull in help from one of the tool wrapper authors, ping @simonbray.