[gmx-users] Difference in hydrogen bonds between different softwares

larif sofiene larifsofiene at gmail.com
Sat Oct 29 12:22:40 CEST 2011

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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