VMD-L Mailing List
From: matt wessel (wesselmd_at_gmail.com)
Date: Wed Jan 04 2017 - 18:05:20 CST
I figured you'd have the simple answer that I was overlooking - thanks!
On Wed, Jan 4, 2017 at 3:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, Jan 4, 2017 at 5:32 PM, matt wessel <wesselmd_at_gmail.com> wrote:
> > Hi all,
> > I am seeing odd behavior when I use the topo readlammpsdata <file> full.
> this is not odd, it is intentional. data files contain image flag
> information, so it is possible to properly reconstruct unwrapped
> coordinates. this is preferable to throwing this information away (as
> it is done when dumping .xyz files with wrapped coordinates). if you
> absolutely want the wrapped coordinates, it is easy to obtain them via
> pbctools. however, the opposite is much more difficult.
> in general, i consider .xyz files a file format of last resort as they
> drop useful information about the system. if you would dump your
> trajectory in atom style dump files or custom dumps with either x y z
> and ix iy iz properties included or xu yu zu, you can get the same,
> plus you have box information and timestep etc.
> in short, this is all well and useful.
> > I run my simulations with LAMMPS (periodic boundary conditions), I am
> > dumping both an xyz and LAMMPS data file at regular intervals. I find
> > when I read a given xyz file to VMD, I get my system as I would expect
> > all atoms confined within the defined periodic box of the system(xlo,
> > 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
> > ensure that each molecule is moved so that no bonds are ever spread
> > 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
> > the topotools documentation at Axel's topotools web pages, and did not
> > 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
> > 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
> > file and create a new xyz file, I get an identical looking system in VMD
> > 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
> > 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
> > 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
> > 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
> > OS 10.11.6 (El Capitan)
> > Thanks for any thought/advice/help
> > Matt
> 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.