[gmx-users] Fwd: genconf / genbox order

Kurt Seefeldt seefeldt at umich.edu
Wed Jun 11 16:53:00 CEST 2003


I'm trying to generate a box with 8 small molecules surrounded by 
water. I have the .gro .top. itp files for the small molecule and have 
generated 1 box with water already, so I know that that works. To make 
the system with 8 small molecules, I tried to genconf the small 
molecule with -nbox 2 2 2 then genbox to add waters. The waters are 
only in the center of the final box. I tried genbox on 1 molecule then 
genconf on that, but that results in random molecules that do not 
represent my original molecule.

Is there an easy way to do this? I could generate a water box and then 
add the small molecules by hand, but I was hoping for a more automated 
way to do this since I have many systems to look at.

Thanks for any help,

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