[gmx-users] Remove PDB and center the protein.

[dipak sanap]

HI all,

I have simulated protein in a dodecahedron box. I know trjconv can be used
to center the protein and remove PBC but I am confused.

I have tried few cases as follows.

Case 1
trjconv -f *.xtc -s *.tpr -center -o centered.xtc
trjconv -f centered.xtc -s *.tpr -pbc mol -ur compact -o centered_noPBC.xtc

Case 2
trjconv -f *.xtc -s *.tpr -pbc mol -ur compact -o noPBC.xtc
trjconv -f noPBC.xtc -s *.tpr -center -o centered_noPBC.xtc

Case 3
trjconv -f *.xtc -s *.tpr -pbc mol -ur compact  -center -o
centered_noPBC.xtc

In all cases, I use protein for centering and system for output. Only third
case keeps protein in center without jumping. What is the best way to
correct trajectory for both visualization and analysis?

Regards,
Dipak