VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 19 2015 - 16:03:03 CDT

On Fri, Jun 19, 2015 at 2:43 PM, Mercer, Brian S. <mercer9_at_llnl.gov> wrote:
> 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.

a better choice would be to use the native LAMMPS dump format. .xyz
files are the lowest common denominator and a lot of information is
lost, e.g. periodicity.

> 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?

why use VMD for this kind of analysis, when you can get it directly
from LAMMPS with the fix reax/c/species and fix reax/c/bond tools.
please note that VMD - unlike the LAMMPS internal tools - cannot take
any kind of periodicity into account for the steps you describe.

> 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?

as mentioned above, this can be computed more accurately (based on the
computed bond order) during the simulation and output to a file
directly from LAMMPS.

it may be worth thinking about a way to read this file into VMD and
then use some additional Tcl script magic to apply this information to
the trajectory frames.

axel.

>
> 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
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.