[gmx-users] system size vs box size

Senthil Kandasamy senthilk at engin.umich.edu
Tue May 21 15:10:59 CEST 2002

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. 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.

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???

any help would be appreciated.


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