From: matt wessel (
Date: Wed Jan 04 2017 - 16:32:11 CST

Hi all,

I am seeing odd behavior when I use the topo readlammpsdata <file> full. As
I run my simulations with LAMMPS (periodic boundary conditions), I am
dumping both an xyz and LAMMPS data file at regular intervals. I find that
when I read a given xyz file to VMD, I get my system as I would expect it,
all atoms confined within the defined periodic box of the system(xlo, xhi,
etc), but of course with bonds for some bonded atom pairs straddling the
boundary so "wrapping" to the other side (dynamic bonds of course nicely
takes care of that visualization situation) . However, when I use topo
readlammpsdata <file> full, I get a different looking system, where it
appears as if topotools has done some sort of detection of bonded atoms to
ensure that each molecule is moved so that no bonds are ever spread across
any periodic boundaries. In fact it's as if the periodic boundaries are
being ignored or at least used to redefine the coordinates. I looked
through the topotools documentation at Axel's topotools web pages, and did
not find any reference to this behavior (I may have missed it), and I also
looked through the VMD mailing lists and saw nothing about this (I may have
missed it here as well - but I try to make sure I do both first before
posting - so if I did miss it, politely point it out and I'll read).

What I can confirm is that if I extract the XYZ coords from the LAMMPS data
file and create a new xyz file, I get an identical looking system in VMD as
compared to the xyz file LAMMPS generates on its own, so I know the XYZ
coordinates and atom types between xyz and LAMMPS data files taken at
identical intervals are the same.

Interestingly, I also tried the command using Axel's HDPE example in his
"Odds & Ends" section of the TopoTools page, and with his HDPE example data
file, I do not see a "vanishing" boundary box, I get a cube with bonds
straddling the periodic boundaries, and it looks just like the image on
Axel's page. I'm just perplexed as to what is actually happening with my
(admittedly much larger) system.

Also, it's not as though the behavior is "wrong", I'm not at all inclined
to call this a bug. It produces a rather nice looking result, and I have
spot checked that the conformations of the individual molecules are not
being altered, just their translational position in space with respect to
each other has been altered relative to the original xyz file. I am happy
to provide images/xyz/data files for others to better understand/try to
reproduce, but they are rather large files (20-40 MB) and I 'm not sure
what the VMD-list scrubbers might do to them.

For reference, I am running VMD 1.9.3 with Topotools v 1.7 on a Mac running
 OS 10.11.6 (El Capitan)

Thanks for any thought/advice/help