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From: Phelan Jr, Frederick R. Dr. (frederick.phelan_at_nist.gov)
Date: Thu Mar 29 2012 - 14:31:58 CDT

I am using the following procedure to draw LAMMPS output with bonds in VMD:

1) Read in the LAMMPS data file: topo readlammpsdata <LAMMPS Data File ".data"> full|molecular|bond
2) Write bond topology to psf file: animate write psf <file.psf>
3) Delete all existing molecules in memory
4) Read in the LAMMPS trajectory file < LAMMPS Trajectory File ".lammpstrj">
5) Read in the psf file: animate read psf <file.psf>

Works great for unwrapped trajectories. However, is there any procedure/trick to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping?

Thanks,
Fred

________________________________
Frederick R. Phelan Jr., Ph.D.
Complex Fluids Group
Polymers Division
National Institute of Standards and Technology
________________________________
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