Rigid body problem

Dear Lammps Community,

I am trying to use ‘rigid’ command to treat CO2 molecules as rigid bodies. I am using the manual (http://lammps.sandia.gov/doc/fix_rigid.html) and some examples from the mailing list. I was able to create a bunch of rigid molecules, but unfortunately they are treated as ONE rigid body. Two most important lines from the log file are shown below:

Dear Lammps Community,

I am trying to use 'rigid' command to treat CO2 molecules as rigid bodies. I
am using the manual (http://lammps.sandia.gov/doc/fix_rigid.html) and some
examples from the mailing list. I was able to create a bunch of rigid
molecules, but unfortunately they are treated as ONE rigid body. Two most
important lines from the log file are shown below:
--
fix RIGID_CO2 GROUP_CO2 rigid/nvt molecule temp 300 300 100
1 rigid bodies with 24 atoms
--
Could you please give me a hint how to divide CO2 molecules and treat them
as separate rigid bodies?

do your individual molecules have different molecule ids? when you use
the molecule flag, the molecule id decides how to group the rigid
bodies; there is no checking whether those are actually connected by
explicit bonds or not (this is so you can also use it with potentials
that have no explicit bonds like tersoff).

axel.

Dear Axel,

do your individual molecules have different molecule ids?

I have set for each molecule different ids manually and it works!
Thank you very much.

There is another question:
I use Topotools for creating data file as it was written in the tutorial:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2#TOC-Step-2a:-Methane

Topotools creates the same molecule ids for all molecules replicated. How could it be possible to create an unique id for each molecule using Topotools?

Thank you.
Kind Regards,
Evgeniya

Kind Regards,

Dear Axel,

do your individual molecules have different molecule ids?

I have set for each molecule different ids manually and it works!
Thank you very much.

There is another question:
I use Topotools for creating data file as it was written in the tutorial:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2#TOC-Step-2a:-Methane

Topotools creates the same molecule ids for all molecules replicated. How could it be possible to create an unique id for each molecule using Topotools?

topotools just uses the information that you feed it. for the molecule
id it uses the resid property in VMD, which in turn is read from the
input coordinates, if present.
if all atoms have the same residue id, you have to overwrite it. this
can be done with a little VMD scripting using the "fragment" index. so
before writing out the data file do:

mol reanalyze top
set sel [atomselect top all]
set resid {}
foreach r [$selc get fragment] { incr r; lappend resid $r }
$sel set resid $resid

for more details on this, please see the VMD user's guide.

axel.

Dear Axel,

Thank you very much for your help! Everything works.

Kind Regards,
Evgeniya