[gmx-users] protein not centered in solvent box

jayalakshmi sridhar jayasri1969 at gmail.com
Mon Sep 14 21:34:59 CEST 2009

I was under the impression that -box and -d should center the protein in the
solvent box. It says in the manual- Center molecule in box (implied by -box
and -d)

On Mon, Sep 14, 2009 at 2:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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. :-)
> Mark
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