I figured out what the problem is with your earlier email.
It is that you are running fix rigid, writing a restart file, then
trying to replicate the system from the restart file.
This comment in the manual applies (doc/fix_rigid.html)
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a
periodic boundary. They are not incremented/decremented as they would
be for non-rigid atoms. This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly. For example, the fix msd will not
compute the expected mean-squared displacement for such atoms, and the
image flag values written to a dump file will be different than they
would be if the atoms were not in a rigid body.
What is happening is that the periodic image flags for atoms in a rigid body
are not what the replicate command expects and hence it can
not create new bonds appropriately.
I'd have to think whether it is easy or posible to fix this, b/c the
replicate command doesn't really know
anything about rigid bodies. Since there are other ways to generate a
system (e.g. write your own pre-processing code that uses a restart or
I'm inclined to just flag this as a restriction on using the replicate command
in conjunction with fix rigid (if there are bonds between 2 rigid bodies).
Also, I see that your data file defines bonds between atoms within some of
the rigid bodies. These might also cause problems for the replicate command.
These bonds are unneeded since the body is rigid. However even if you
get rid of these I think you will still have the problem for bonds between atoms
in 2 different rigid bodies.
Does this make sense? Do you have some other work-around to create the systems