[gmx-users] how to center the protein?

[Albert]

Dear:

   I am using the command:

trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol

trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans

to extract a frame of my md simulation and I found my protein is not in 
the centre of simulation box. here is a figure for it:


https://dl.dropbox.com/u/56271062/position.jpg

as we cab see the protein is just in the corner of box and the water 
molecules (lefft sphere) in the protein was separate from protein and on 
the otherside of box.

THX
Albert