Atom group charges from LAMMPS simulation

[Alexandra Ringsby]

Hello MDAnalysis users,

I noticed something odd today when attempting to print the charges of certain atom groups that I have defined. I read in the documentation that atom groups selected via the select_atoms command should contain information regarding the charges of atoms in the group, provided that partial charges are assigned in the topology. 

I do assign partial charges, so I would expect that my atom groups would contain charge data. However, I found today that only certain groups display accurate charge data. For example, one of my selections is a singular cation. In the topology, the atom type is set to have a charge of 1.0, and, as expected, the charges attribute returns a value of 1.0. However, my other selections (two different moieties of a polyanion) return erroneous charge values of 0.0. Is there any obvious reason why this might be occurring?

Best,

Alexandra 

[Oliver Beckstein]

Hi Alexandra,

welcome to the MDAnalysis list!

How did you load your LAMMPS trajectory, specifically how did you create the Universe? What are the input file formats? How are the charges stored in your input files?

Oliver

[Alexandra Ringsby]

Hi Oliver,

It looks like I was actually creating my universe with method that didn't load the charges. Problem solved! Thanks anyways!

Best,

Alexandra