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
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