[gmx-users] protein not centered in solvent box

[Justin A. Lemkul]

jayalakshmi sridhar wrote:
> 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)

Yes, that is the help info for the -c option, which centers the molecule in the 
box "implied by -box and -d."

Also realize that an octahedral box in VMD is represented as a rectangular box. 
  To correctly see the system, you need to use trjconv.

-Justin

> Jaya
> 
> 
> On Mon, Sep 14, 2009 at 2:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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