GROMACS version: 2019
GROMACS modification: Yes/No
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Hi guys,
This is my problem when i run MD simulation. I have run MD simulation, however, when i check files: nvt.gro, npt.gro, md.gro, i see that protein is ejected out of the box and ligand also (like a picture that i sent below). Results of md.log, npt.log and nvt.log are normal and they completely finish.
It would be great if you guys can tell me what is my problem and how to fix them. Thank you so much.
Nhina.
probably pbc issue-
check out gmx trjconv
i did it thank you very much