[gmx-users] protein broken

ithu ithu19 at gmail.com
Sun Aug 1 19:48:15 CEST 2010

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

If anyone could have a answer to this problem, I would be very grateful.


El porvenir está en los huevos: bobbyybobby.blogspot.com
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