[gmx-users] Using editconf to center on 0 0 0 , then using genbox

[Arneh Babakhani]

I'd like to have my structure centered on 0 0 0 .

The solvated structure is completely off.  My protein is at the center,
but the solvation shell is way off center.

I just dont understand why genbox isn't recognizing the previous editconf
step.

Ok, I'll try solvating first then using editconf.


> Arneh Babakhani wrote:
>> Hi,
>>
>> I'm using editconf to center my sytem about the origin (0 0 0).  No
>> problem there.
>>
>> But then when I use genbox to solvate the resulting structure, the
>> solvent
>> is offset (not centered about 0 0 0).   Is there a way to correct this?
>
> Have you tried editconf on the solvated structure? Why does it matter
> anyway?
>
> Mark
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