[gmx-users] system size vs box size
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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