[gmx-users] how to center a MARTINI trajectory so that the lipid bilayer remains at the center of the box

[maria goranovic]

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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