GROMACS version:2023.2
GROMACS modification: Yes/No
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hello,
I have used these two commands to fix two separate DNA strands.
gmx trjconv -f file.xtc -s file.tpr -pbc cluster -o file-cluster.xtc
gmx trjconv -f file-cluster.xtc -s file.tpr -pbc mol -center -o file-cluster_center.xtc
and for further visualization i used file-cluster_center.xtc. in the system i have only DNA , water molecules and ions for notarization. is it correct? do I miss any information?