VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 19 2015 - 16:11:54 CDT

On Fri, Jun 19, 2015 at 3:55 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Brian,
>
> 1.) Can you use three separate representations? For instance if you had
> atoms of type A, B, and C, you could have one representation for "type A B",
> one for "type B C", and one for "type A C". Its perfectly possible that it
> won't look right, but at the very least each of the representations can be
> set to have a difference distance cutoff, and that might be what you are
> looking for.

there is a known problem with this approach: with "type A B" you not
only capture A-B bonds but also trigger A-A and B-B and similar for
the others. if the cutoff is particularly long, you'll get a lot of
bonds.

> 2.) Aren't you basically asking the question of "are these two things close
> together?" a whole bunch of times? I would use the "measure contacts"
> (http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html) command to get
> me the full list of atoms of a certain type that are within some cutoff of
> one another (if pbc is an issue, exwithin will probably need to be used, and
> the scripting gets more involved). These lists would shrink with time as the
> number of bonds shrinks, and that would I think be the easiest way of
> getting a numerical answer as to how many bonds have been broken. You could
> also keep track of which are the bonds that break this way by analyzing the
> lists. The caveat here is that measure contacts works on things that aren't
> bonded, so you'd need to clear the automatically generated bondlist first
> (with topotools for instance) to have it do what you want.

the problem with ReaxFF calculations is that what is considered a bond
is not directly determined by a distance cutoff, but rather by the
bond order. there is some correlation between the two, yet if one
wants reasonably accurate and consistent information, one needs to
consider the parameters that are also used as input in the ReaxFF
simulation. as i mentioned on my other response, LAMMPS has such a
facility built in. so this analysis is mostly a matter of writing a
perl/python/whatever script to post-process the file with the bonding
information generated during the simulation.

axel.

> In general, VMD's programming assumes that bonds are not dynamically made
> and broken, so its going to be unwieldy to go around changing what was meant
> to be an unchanging topology on a per frame basis.
>
> -Josh Vermaas
>
>
> On 6/19/15 1:43 PM, Mercer, Brian S. 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.
>
>
>
> 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
>
>
>
> 

-- 
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.