problem in the atom coordinates exceeding the box length

Dear all lammps-users,

There are 100 hexadecane molecular in the system. Now I need to measure the direction of every chain to check whether some of them are parallel. I used the end to end atom coordinates to represent the vector of each chain. The problem is that I cannot use the atom coordinates to measure the direction when it exceed the box periodic boundary. I have tried to use unwrapped atoms, but seems like the molecular distribution is different from wrapped atoms.

Does anyone can help me to solve this problem? Thank you very much.

Best regards,


Are you asking about a post-processing step?

If you compute your vector from unwrapped coords, it should be correct,
so long as you started the simulation with correct image flags (e.g. in your data file)
for any molecule which was overlapping the periodic box to begin with.

If I undestand, the direction of the vector is all you care about and it
will be correct when the 2 end atoms are unwrapped.