What is the problem exactly? The two layers separate over the pbc?
did you try a -pbc nojump prior the centering?
On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
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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