VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 24 2010 - 17:02:38 CDT

On Sun, 2010-10-24 at 08:45 +0900, Aric Newton wrote:
> vmd-l users,
>

aric,

> 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

any changes like this would have to be made to the source
code to the molfile plugin that reads .mdf files.

if you can upload the problematic file(s) to the VMD biofs
into the testfiles directory, somebody can take a look at
it. other than that, you are on your own. the plugin refers
to mdf specifications from 1998 as documentation, so perhaps
your file has features that confuse that VMD plugin.

the same goes for the .xsd format, which will most likely
require writing a new plugin, which in turn requires a
reasonable documentation and a selection of example files
as well as a person with the ability to program such a
plugin and the time and interest to do it.

[...]

>
> 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?

these issues should have been corrected in the latest alpha
test versions of VMD. unfortunately, there are currently only
precompiled versions for linux and solaris.

you can update your topotools plugin from here:
http://sites.google.com/site/akohlmey/software/topotools

and download an updated lammps molfile plugin source from here:
http://sites.google.com/site/akohlmey/software/lammps-icms

check out the attached archives. please let us know if you
have problems compiling installing those.

i'd be interested to see your files, if you still have
problems with the updated plugins.

cheers,
    axel.

>
>
> Your advice and input is appreciated.
>
>
> Thank you,
>
>
> Aric 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.