[gmx-users] get a box of 100 molecules

Adrien Delmont adriendelmont at yahoo.com
Wed Mar 11 16:45:36 CET 2009

Dear Users,

I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted to ask it to the users. 
Can I get a box of 100 molecules that are randomly distributed and not attached to each other using the commands below? 
If there are something wrong in commands please share your valuable suggestions with me.   

Thanks in advance


pdb2gmx -f mol.pdb -o mol.gro -p mol.top -i mol.itp ( then chose suitable force field )

genbox-ci mol.gro -nmol 100 -o 100mol.gro -p 100mol.top -box 12 12 12

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