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

dipak sanap dipak94sanap at gmail.com
Tue Aug 23 08:42:22 CEST 2016

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

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?


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