[gmx-users] system size vs box size

[Anton Feenstra]

Senthil Kandasamy wrote:
> 
> I have been manipulating  a large pdb file.
> While using editconf, I get the following
> 
>      system size :  6.612  6.636  4.082 (nm)
>      center      : -0.000  0.000 -0.000 (nm)
>      box vectors :  6.418  6.444  6.596 (nm)
>      box angles  :  90.00  90.00  90.00 (degrees)
>      box volume  : 272.81               (nm^3)
> 
> I notice that the system size and the box size are different.
> 
> I guess the system is found by actually calculating the coordinate
> extremes in the x, y and z axes of the pdb file, whereas the box vectors
> are simply copied from the CRYST line of the PDB file. 

Correct.

> I removed a few
> layers of water in the z-direction and hence about 2.5 nm has been cut
> off in the z-direction.It makes sense.
> However, what could be the reason for the slight discrepancy in the x
> and y coordinates? How will that affect the simulations.

What do you mean by 'discrepancy'? With what? Do you mean that the
x, y and z dimensions are not the same? In that case it is simpy
because you didn't tell editconf to make a cubic box.

> Can I re-edit the pdb or gro file to reflect the new system size? i.e.
> replace the CRYST line with the new system size values?
> 
> or am I missing something important here???

Yes: periodicity. Molecules are always whole (at least, in Gromacs),
with their geometrical center inside the box. That means that atoms
can (or actually, will) stick out of the box, on all sides. This in
turn means that your system size (as defined by editconf in the way
you describe correctly) will ALWAYS be larger than your box size.
This is no problem and should generally not be 'corrected'.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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