[gmx-users] image centering

Myunggi Yi myunggi at gmail.com
Tue Dec 25 22:48:29 CET 2007

Dear users,

I have a membrane simulation trajectory,
in which the solvent (water and ions) is separated by lipid bilayer.

I want to center the solvent so that the membrane is separated by two layers
at the bottom and top in the unit cell.

I have tried the followings.

trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster
trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx
-center rect -pbc whole

Both pbc and center didn't work.
Is there any way to center the solvent?

Happy holidays.

Best wishes,

KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
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