Dear All, This has been discussed before for individual frames. But I am having a problem in trying to center a trajectory so that the bilayer remains at the center of the box. I have tried several combinations, but none of the them work. In each case, the centering and/or the fitting is done on the lipid bilayer itself.
trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -center -boxcenter zero -pbc mol this one works for one particular .gro file, but not for the whole trajectory. I tried all of the following, but none of them work. What is the solution ? trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans -center trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -pbc mol -fit trans -center -boxcenter zero trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit trans trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -fit progressive -- Maria G. Technical University of Denmark Copenhagen
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