[gmx-users] Increasing system size

Viswanadham Sridhara muta.mestri at gmail.com
Mon Oct 10 03:31:57 CEST 2005

Hi Gmx users,
I have fairly simple question.
I have a system of DPPC bilayer with water on the top and bottom. I was
wondering whether there is any way to increase the system size in
Z-direction and filling them with waters i.e., initially If i have 6 by 6
by 6 nanometer cube, with 1nm of water above and below the bilayer, what is
the easiest way to make it 6 by 6by 10nm(increasing waters to 3nm above and
below). If I remove waters initially, increase the system size to 6 by 6 by
10, and then solvate it using genconf -cp aaa.gro -cs conf.gro , the
problem is that there are waters inbetween the bilayer.And I believe I have
to run MD until all the waters go out of the bilayer.
I thought maybe there is genconf or some routine may help me, but I dont
know how?
Thanks in advance.
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