Read LAMMPS trajectory file when the number of atoms is not same as that in topology file?

[karpathyan]

Hey,
I'm running a LAMMPS simulation with 2197 atoms, when writing the trajectory file, I only write the information of atoms that enter a specific region in the simulation box. Because of this the number of atoms in the traj file is less than the total number of atoms defined in the toplogy file. Hence I'm getting the error:

ValueError: The topology and LAMMPSDUMP trajectory files don't have the same number of atoms!
Topology number of atoms 2197
Trajectory: dump.gz Number of atoms 1

How can I load this type of files ? Thanks for any help.
Here is how I load this:

import MDAnalysis as mda
u = mda.Universe('datafile.data', 'dump.gz', format='lammpsdump')

[orbeckst]

Unfortunately, MDAnalysis does not handle grand canonical simulation data at the moment.

If this is a feature that would help your work, please add your use case to the (long standing) issue #864 .

You may be able to hack a GC-version of MDAnalysis with the use of "ghost particles" that act as place holders for particles.

• Generate a universe with the maximum number of particles.
• Add a topology attribute like "ghost" that is False if the particle has coordinates and True if it should be ignored. (The chapter in the user guide on Adding custom TopologyAttrs is currently empty – sorry – so you have to dig into the Topology system)
• Write an on-the-fly transformation that reads your dump file at each step and then places the atom coordinates into the arrays of the timestep; mark any empty spots as a ghost particle.
• In your analysis, always filter your atoms to have "ghost = 0" or something like that.

It's a lot of work. However, you may then already be well on your way to have written a cool extension of MDAnalysis!