[gmx-users] fix a group in truncated octahedron

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Dec 27 18:14:22 CET 2009

Hi Wende, please do not double post. If you are unsure if your post  
got through, you can easily see the list at  

You did not put units beside 40, so I suppose that you mean 40 A,  
whereas gromacs uses nm.

1. Make a box with one sodium ion and then editconf -c -d 4 -bt  
dodecahedron. This will give you your box, then you can put your  
lattice inside it. With properly selected atom in an index file, you  
could easily do this in one step based on the commands above (plus the  
index group with a single central atom).

2. This is clearly laid out in the manual under energygrp_excl. You  
should familiarize yourself with the online .mdp file options at  
http://manual.gromacs.org/current/online/mdp_opt.html which will help  
you find such things.


-- original message --

Hi GMX users,

I want to fix a group in a truncate octahedron. How can I dealt with the
questions below,

1. I hope the box corresponds to an inscribed circle of cubic of size
40*40*40, how to calculate the box vectors?

2. One spherical rigid body consists of  face-center cubic lattices is fixed
in the center of the box. I do not want to calculate the force and energy
between the paritcles of this rigid body, so that no matter how large force
between them shoud not blow up the rigid body.   How can I do this?

Thanks in advance.

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