[gmx-users] problems about trjconv

Di Pan dpan at uab.edu
Thu Nov 22 23:15:05 CET 2007

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

Thank you very much



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