[gmx-users] fix a group in truncated octahedron

[lammps lammps]

Sorry for this.

Thanks for your kind reply.  That is the answer of my question.

Actually, I only want to make sure whether the command of energygrp_excl has
the ability not to calculate the force in the group.

The manual about energygrp_excl seems not talk about how to deal with the
force. Maybe, I do not fully understand this command.

------------------------------------------------------------------------------------
energygrp excl:
Pairs of energy groups for which all non-bonded interactions are excluded.
An example: if
you have two energy groups Protein and SOL, specifying
energygrp excl = Protein Protein SOL SOL
would give only the non-bonded interactions between the protein and the
solvent. This is
especially useful for speeding up energy calculations with mdrun -rerun and
for excluding
interactions within frozen groups.
---------------------------------------------------------------------------------------

Happy new year.


2009/12/28 <chris.neale at utoronto.ca>

> Hi Wende, please do not double post. If you are unsure if your post got
> through, you can easily see the list at
> http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html.
>
> 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.
>
> Chris.
>
> -- 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.
> --
> wende
>
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-- 
wende
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