GROMACS version:2021
GROMACS modification: Yes/No
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Hello dear friends. In Gromacs after energy minimization, I found that some hydrogen atoms are separated from the structure, what is the cause and how should it be eliminated?
This is almost certainly a simple periodicity issue. Make molecules whole with trjconv.
How used trjconv for em step output?
What does your consultation of the documentation tell you?
(Note that this is an issue addressed every week on this forum; you can easily get an answer by searching)