[gmx-users] Genbox to generate box with isolated molecules...

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 1 03:51:29 CEST 2010

Tandia, Adama wrote:
> Dears,
> I'm generating a box filled with NO3 molecules using Gromacs 3.3:

Any particular reason you're using software that is five years old?  Unless 
you've got a particular reason (i.e. continuity with older work), I'd strongly 
recommend upgrading to version 4.0.7 for all the newest features and a major 
speed upgrade.

>  genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0
> -nmol 800 -vdwd 0.2
> The file bigbox.gro is generated but molecules are entangled. This makes
> the geometry optimization to remove close contact impossible.
> Any suggestions?

Have you tried a bigger box?  Using a 5-nm box worked for me.  When I tried the 
same command you did, my machine ran out of memory, so it's probably a rather 
complicated task and thus might not be a suitable application for this 
particular tool.

Have you tried using genconf instead?  With genconf you can easily build a 
lattice of NO3 that you can then equilibrate; genbox will try to randomize the 
configuration, but you can do it yourself with sufficient equilibration anyway.


> Thanks,
> Adama
> Adama Tandia, Corning INC, SP-TD-01-01 Corning NY 14831 USA, Tel: 607
> 248 1036 -GoogleVoice: 708 433 9430


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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