[gmx-users] fix a group in truncated octahedron

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 31 09:45:31 CET 2009

lammps lammps wrote:
> 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.
> ---------------------------------------------------------------------------------------

Energies and forces are evaluated very close together in "code execution 
time", since they are often functions of the same quantities and this is 
the most efficient way to calculate both. Thus they are regarded as 
somewhat synonymous in the documentation. Presumably the definition of 
energy groups early in the manual is clear on this point. Thus the use 
of energy group exclusions excludes the calculation of both energies and 
forces as appropriate. I believe it is impossible with GROMACS to 
evaluate a force without evaluating the corresponding energy, for what 
that is worth.


> 2009/12/28 <chris.neale at utoronto.ca <mailto: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
>     <mailto: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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> -- 
> wende

More information about the gromacs.org_gmx-users mailing list