[gmx-users] image centering

[Myunggi Yi]

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,

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

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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