[gmx-users] How to explain the phenomenon of -genbox?

[maggin]

Hi,

I use : genbox -cp box.6_newbox.gro -cs spc216.gro -o box.6_solv.pdb -p
box.6.top

Output configuration contains 301821 atoms in 100053 residues
Volume                 :     3030.92 (nm^3)
Density                :     1000.12 (g/l)
Number of SOL molecules:  99801

When I use VMD to see the structure of box.6_solv.pdb, it some strang, the
picture is as follow,

<http://gromacs.5086.x6.nabble.com/file/n5015927/%7BXRW%29NI8%40%29IN_6%5D%7BE%25K3D%40B.jpg> 

What I get from genbox is right?

Thank you very much!

maggin

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