VMD-L Mailing List

From: Mercer, Brian S. (mercer9_at_llnl.gov)
Date: Fri Jun 19 2015 - 13:43:41 CDT

Hi VMD users,

I am doing ReaxFF simulations of a crystalline polymer undergoing fracture, and am seeking a way to visualize the bond-break behavior, as well as track which bonds have broken over time. I am new to using VMD but it seems like it has a lot of the tools in place to do this, though I'm currently stuck on a few fronts.

I'm currently doing simulations in LAMMPS and dumping the trajectory to an xyz file to read into VMD.

1) Is there a way to assign different bond cutoff lengths to different types of bonds in the visualizer? DynamicBonds works well for visualizing except that the bond cutoff is universal. I am interested in 3 distinct bond types in the system, each of which breaks at a different length. I see that you can assign bond topology explicitly using topotools - can perhaps I make the visualizer draw bonds according to that topology, and "delete" bonds that exceed the cutoff criteria?

2) In addition to visualizing, I'd like to keep track of how many bonds (and of which type) have broken over the course of the simulation. Similar to how the hbonds.tcl script can be used to plot the number of hydrogen bonds present in each frame. I'm again thinking this could be done by assigning an initial bond topology and removing bonds from the system as they exceed a specified distance criteria based on their type. Or, does VMD already provide such a functionality?

Please let me know if you have any thoughts on how I might proceed.

Thank you,

Brian 

--
Brian Mercer
Lawrence Livermore National Laboratory
University of California Berkeley
Lawrence Graduate Scholar and PhD Candidate