VMD-L Mailing List

From: Aric Newton (agnewton_at_berkeley.edu)
Date: Sat Oct 23 2010 - 18:45:06 CDT

vmd-l users,

I am trying to use VMD for to produce some animations of my MD
simulations that I conducted using a combination of Materials Studio
(to build the structure) and LAMMPS (for the calculations). The
problem I am having is with the importation of the structure files to
describe the model where I will then load the LAMMPS trajectory data.
I have tried two approaches using 1) Materials Studio files for
structure and 2) LAMMPS data and trajectory files. I describe them
below. I would be happy if only one of the approaches worked and I'd
like to ask for some advice from the users who have succeeded at this.

Approach 1
Referring to archived posts (Wednesday, August 11 2010; Volume 01 :
Number 1657), I attempted to load first the *.mdf (structure) and then
*.car (coordinate) files from Materials Studio. When loading the
*.mdf file, I get an error due to the "namelist index value being too
large" (message reproduced below) and the process is aborted. Is
there away to set the "larger index types" when compiling VMD? The
namelist index value at the time of overflow is 1851. I am using the
pre-packaged VMD for MACOSXX86, version 1.8.7 (August 1, 2009) and
didn't recognize that option during installation. My system isn't
that large (6408 atoms), but I tried a smaller version of the model
without the hydration shell (no. atoms 1470). Reading the *.mdf
(structure) file, the mdfplugin "Could not find atom in hash table"
and vmd reported an "Error reading bond information". This wasn't
completely fatal, as I could load the *.car (coordinate) file into the
molecule (car plugin reported no errors), but there were no bonds. Is
this an issue that I can solve by increasing the atom index value
somehow? Or is it an issue with the plugins/ files? The import files
were created with Materials Studio 5.0 (and not Insight II) which
still uses an *.mdf file for structure but an alternative format
(*.xsd) for coordinates with an option to "export" the file in *.car
format (which I did).

Approach 2
Using the TopoTools plugin, I loaded the initial data file for my
LAMMPS simulations with the readlammpsdata <filename> command. The
structure was imported accurately, but when I load the trajectory data
into the structure and animate the trajectory, I get abstract art.
Namely, from frame zero (imported structure) to one (trajectory), the
model is rendered as random line art with a definitive x-y grid
pattern of voids. I presume that the atom indexes become mixed as a
result of the way that LAMMPS keeps track of the atoms and dumps them
to the trajectory which is not in order of the atom indexes but by
processor (the voids in the abstract line art are from dividing the
atoms by processors (?)). Is my presumption accurate and is there a
procedure I am overlooking when trying to merging LAMMPS data and
trajectory files that solves this problem?

Your advice and input is appreciated.

Thank you,

Aric