Greeting I'm doing a MD simulation of a monomeric protein and i got different results about hydrogen bonding from what another team has found (they use other MD software ) , for example i find a Hydrogen bound between K 77 - Asp 81 and they find K 77 - R 82, my question is : Is hydrogen bounding different from one simulation to another (with the same running time) and if not are hey different from one software to another ? If so, when publishing results is it scientifically credible to publish value that are different arguing that internal gromacs mechanism of computation are different then their home-built software? thank for responding and good work , Gromacs is really great piece of art :) .
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