Fix rigid group syntax clarification

In fix rigid example in docs:

fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off

clump1, clump2, clump3 are the group id of atoms i want to behave as
rigid body, what is 'fluid' ?

i.e in the following simulation:

group clump1 index id 1:20
group clump2 index id 21:40
group clump3 index id 41:60

fix 2 fluid rigid/nvt group 3 clump1 clump2 clump3

what group does "fluid" group id represent?

In fix rigid example in docs:

fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off

clump1, clump2, clump3 are the group id of atoms i want to behave as
rigid body, what is 'fluid' ?

i.e in the following simulation:

group clump1 index id 1:20
group clump2 index id 21:40
group clump3 index id 41:60

fix 2 fluid rigid/nvt group 3 clump1 clump2 clump3

what group does "fluid" group id represent?

from the fix rigid documentation:

For bodystyle single the entire fix group of atoms is treated as one
rigid body. This option is only allowed for fix rigid and its
sub-styles.

For bodystyle molecule, each set of atoms in the fix group with a
different molecule ID is treated as a rigid body. This option is
allowed for fix rigid and fix rigid/small, and their sub-styles. Note
that atoms with a molecule ID = 0 will be treated as a single rigid
body. For a system with atomic solvent (typically this is atoms with
molecule ID = 0) surrounding rigid bodies, this may not be what you
want. Thus you should be careful to use a fix group that only includes
atoms you want to be part of rigid bodies.

For bodystyle group, each of the listed groups is treated as a
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body. This option is only allowed for fix rigid
and its sub-styles.

in short, fix rigid only acts on atoms in the group fluid, i.e. the
"fix group". so the rigid bodies are effectively the intersection of
"fluid" and "clump1", "clump2" and "clump3", respectively.

axel.

In that case what is the difference between:

fix 1 all rigid/nvt group 3 clump1 clump2 clump3 ...

and

group clump_of_clumps union clump1 clump2 clump3
fix 2 clump_of_clumps rigid/nvt group 3 clump1 clump2 clump3 ...

?

will both commands above give equivalent results?
I ask because my system is mixture of rigid and non rigid molecules,
currently I am running it as

"fix 1 all rigid/nvt ...."
"fix 2 non_rigid npt ..."

it does not look right fundamentally. because now i will be
integrating all non rigid molecules twice.

In that case what is the difference between:

fix 1 all rigid/nvt group 3 clump1 clump2 clump3 ...

and

group clump_of_clumps union clump1 clump2 clump3
fix 2 clump_of_clumps rigid/nvt group 3 clump1 clump2 clump3 ...

?

will both commands above give equivalent results?

you are a scientist, right? then you should practice your most
fundamental scientific skills and make a suitable experiment and
observe.

axel.

I am doing that only! But thought about following the traditional path
of literature search and seeking wisdom of the elderly first, in case
it saves time and efforts

1 Like

you are overlooking one little detail here: the "seek the wisdom of
the elderly" path should be taken *after* you have made some (simple)
tests and validations and have questions that you cannot get answer
from the literature for.

asking before may save you some time, but has the consequence of
wasting the time of others that could be better spent on complicated
problems, where the experience is essential. it also projects that you
are not able or are lacking the confidence to teach yourself a skill
on your own and instead need reassurance even before taking
initiative.

so you see, what may seem like a good idea, can also be a bad one. :wink:

axel.