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

Arneh Babakhani ababakha at mccammon.ucsd.edu
Thu Aug 9 04:57:28 CEST 2007

Ok, I don't quite understand something.

My dowloaded pdb file of my molecule is centered at about 3 3 3 (in x y z,

I perform genbox to solvate it: No problem.

I then perform editconf to translate the center of the molecule to 0 0 0
(and move the water likewise):
editconf -f Molecule_Solv.gro -o Molecule_Solv -translate -3 -3 -3
[Note here, I'm not using the -center option, b/c I want to place the
center of the molecule, not the entire system, at 0 0 0].
No problem here (when I load the structure up in VMD and measure its
geometric center, it is indeed at 0 0 0).

But then, when I run a simulation on this structure (say a brief energy
minimization), it reverts back to its original center at 3 3 3.  In other
words, the outputted structure after the minimization has the molecule
centered back at 3 3 3.  Why is this happening???  Does this have anything
to do with the dimensions of the box? (which are 6 6 6).  The dimensions
are irrespective of the centering of the box, right?

[I know this seems a little trivial.  I'd like to have my molecule
centered at 0 0 0, b/c I'll be collecting coordinates later and it'll just
make my math easier.]

> 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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