[gmx-users] Genbox question

Kevin C Chan cchan2242-c at my.cityu.edu.hk
Tue Nov 4 05:39:43 CET 2014

Dear Users,

I am trying to build some starting structures of lipid bilayers for MD using genbox to add waters. For some reasons I have already equilibrated my lipids in a water box previously so it no longer looks like a perfect rectangle, there are “flying tails" at the edges. However I still want to build a typical bilayer-in-water model in which water only appears above and below the bilayer (but not asides) and it should be able to introduce a periodic boundary condition in the x-y plane  (assuming the bilayer’s normal is along the z-axis) afterwards. The problem is as I could not accurately define the dimensions of my equilibrated lipids anymore, how could genbox be used to fill the box as what I expected? 

I will greatly appreciate it if anyone could share your experience on this.


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