[gmx-users] Fwd: genconf / genbox order

David 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:
> Hi,
> 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,
>    Kurt
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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