[gmx-users] protein not centered in solvent box

[jayalakshmi sridhar]

Thanks for the help. With your suggestions I was able to center the molecule
in the box.
Jaya.

On Mon, Sep 14, 2009 at 2:57 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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)
>> Jaya
>>
>
> Yes, but they aren't meant to work in concert. Specifying both the size of
> the box and the distance between the solute and the edges of the box is only
> uniquely defined for a very lucky solute.
>
> Mark
>
>  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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>>
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