Hi, All I do my md simulation for 30ns, but after 20ns the protein move out of the box, so it seems that the protein is broken in .trr file. I try to use trjconv to put the protein back into the box and make the protein whole. The command is like below: trjconv trjc -f *.trr -o out.trr -s *.tpr -pbc nojump -center rect
But after run the trjcov command, some parts of the protein is till out of box, and seems like broken. Is there anyone meed the same problem can tell me how to resolve this problem. Thank you very much Di,Pan Di,Pan
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