[gmx-users] protein not centered in solvent box

jayalakshmi sridhar jayasri1969 at gmail.com
Mon Sep 14 21:05:58 CEST 2009

Dear GROMACS Users,
I am new to GROMACS. I am trying to solvate my protein in a octahedral box.
I used the following commands after generating the initial .gro and .top
$ editconf -f  1z10_groinit.gro -o 1z10_groinit.gro -box 8.5 -d 0.85 -bt
 and then
$ genbox -cp 1z10_groinit.gro -cs -o 1z10_groinit_b4em.gro -p

But when I visualize the solvated protein in VMD, I see that the protein is
not centered in the box. All help is greatly appreciated. Thanks.
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