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.
Mark
2009/12/28 <chris.ne...@utoronto.ca <mailto:chris.ne...@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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