[gmx-users] fix a group in truncated octahedron

lammps lammps lammp2forum at gmail.com
Thu Dec 31 09:22:58 CET 2009

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091231/ee2d0190/attachment.html>

More information about the gromacs.org_gmx-users mailing list