[gmx-users] how to center the protein?

Albert mailmd2011 at gmail.com
Mon Oct 8 11:36:58 CEST 2012


   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:


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.


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