[gmx-users] protein not centered in solvent box

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 14 21:12:11 CEST 2009

jayalakshmi sridhar wrote:
> 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
> files.
> $ editconf -f  1z10_groinit.gro -o 1z10_groinit.gro -box 8.5 -d 0.85 -bt
> octahedron
>  and then
> $ genbox -cp 1z10_groinit.gro -cs -o 1z10_groinit_b4em.gro -p
> 1z10_groinit.top
> 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.
> Jaya.

Well you didn't tell it to center on the protein, so the result should 
be no particular surprise. Read editconf -h and genbox -h and see what 
you learn about how to center things. :-)


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