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

Tandia, Adama TandiaA at Corning.com
Tue Aug 31 23:37:07 CEST 2010


I'm generating a box filled with NO3 molecules using Gromacs 3.3:

 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?


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

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