[gmx-users] Fwd: genconf / genbox order
spoel at xray.bmc.uu.se
Wed Jun 11 17:00:01 CEST 2003
On Wed, 2003-06-11 at 16:51, Kurt Seefeldt wrote:
> 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.
yes, but be more specific please...
maybe your box with 8 molecules has incorrect box size, or maybe you are
specifying a boxsize to genbox whereas you shouldn't.
> Thanks for any help,
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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