[gmx-users] Inhomogeneity of water molecules insertion into the box

Zhikun Cai caizkun at gmail.com
Mon Apr 1 13:55:43 CEST 2013

Hi all,

I would like to add 484 water molecules into the box using command:

 genbox -cp newbox.gro -cs tip4p.gro -maxsol 484 -p topol.top -o

What I expected is those water molecules would be randomly inserted into
the box and the box should appear homogeneous. But the result disappointed
me. Throught VMD, I found that the 484 water molecues was inserted almost
in one half of the box. Then when I added more water molecules, they began
to occupy the other half box.

So what could I do to make the inserted 484 water molecules randomly
positioned in the box in the beginning?
Your advice would be highly appreciated.


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