[gmx-users] how can I create a fcc cell?

Berk Hess gmx3 at hotmail.com
Wed Nov 9 17:06:15 CET 2005

>From: "Manuel Kremer" <manuel.kremer at tu-clausthal.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] how can I create a fcc cell?
>Date: Tue, 8 Nov 2005 14:57:04 +0100
>Dear gmx-users,
>For further DFT studies of my system (simple molecule in a water
>environment) it is necessary to do the gromacs simulation in an fcc
>cell. So I need angles between the basis vectors of 60 degrees. I tried
>the following:
>editconf -f name.gro -o -bt triclinic -box 5 5 5 -angles 60 60 60
>genbox -cp out -cs -p name.top -o b4em
>But if I want to view the result after energy minimalization with ngmx
>or vmd it is still a cubic box (the molecules are partially outside the
>box ngmx draws - even if I choose a triclinic box).
>What am I doing wrong? How do I have to change my editconf and/or my
>genbox parameters?

As long as the angles in the pdb file are 60 degrees and the you have more
than 3 non-zero elements on the last line of your gro file nothing is wrong.
In many cases the visualization will not put the atoms in the box.
If you want to view it this way use:
trjconv -pbc whole -ur compact


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