Hi All! I do my md simulation but the protein moves out of the box, so it seems that the protein is broken in .trr and .xtc 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 -f 18pTTAD-Taz2-water.gro -s 18pTTAD-Taz2-water.tpr -pbc nojump -center -o 18pTTAD-Taz2-water.cen.gro However several residues still seem out of the box and the protein seem broken. When performing g_rmsf those atoms have large rmsf (7 or 8).
If anyone could have a answer to this problem, I would be very grateful. Esteban -- ------------------------------------------------------------ El porvenir está en los huevos: bobbyybobby.blogspot.com ------------------------------------------------------------
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