VMD-L Mailing List

From: Aric Newton (agnewton_at_berkeley.edu)
Date: Fri Oct 29 2010 - 09:16:30 CDT

Hi Axel,

Thank you for looking into the issues I was having with my input
files. I have replaced the mdfplugin and lammpsplugins. Upon VMD
start up, there is a message about these 2 new plugins (see below),
but otherwise all runs smoothly.
...
Found 2 plugins or data handlers in directory
        '/Users/agnewton/Applications/GeochemistrySoftware/VMD/VMD 1.8.7.app/
Contents/vmd/plugins/MACOSXX86/molfile'.

I have followed your recommendation and used the *.psf file that I
generated from the lammps data file and TopoTools and a *.dcd
formatted trajectory for visualization of my trajectories (I wrote
redundant simulation trajectories (a binary and ASCII text) as
insurance). Your attachments at the bottom anticipate the other
unspoken issue. Namely, that my bonds are wrapped around the periodic
boundaries when animating the trajectory. I've been able to unwrap
the trajectories in the past with the PBC tools (pbc unwrap), but as
you stated, it isn't very useful when trying to produce an animation
of the trajectory because the water and ions just wanders out of the
cell. I've been reading the documentation for the PBC tools and
thought that it would be possible (after unwrapping the trajectory
data) to selectively wrap the Na ions and the water molecules in the
image while avoiding bonds across the cell with something like pbc
wrap -sel (Na & H2O) -compound (H2O). I thought that the -compound
option would allow me to specify which atoms will not be wrapped if a
compound (the water) would be split by the wrapping. Your advice
suggests that I have misunderstood the description (I haven't tried
it) and that I should try another avenue (maybe a LAMMPS script to
"unwrap" the trajectory? It's an option when writing the LAMMPS
trajectory, maybe post-simulation, too?).

Thank you again for looking into this. I provided the above
description as background. I'll work on the issue myself and see if I
come up with a solution before posting anything to the list.

Thank you,

Aric

On Oct 27, 2010, at 11:43 AM, Axel Kohlmeyer wrote:

> On Sun, 2010-10-24 at 08:45 +0900, Aric Newton wrote:
>
> hi aric,
>
> a few updates.
>> 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
>
> the first bug in the mdf plugin would be triggered when your
> system has more than 9 "molecules" defined in the .mdf file.
>
>> 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
>
> this was due to the fact, that you had sodium atoms without
> any bonds as part of the first "molecule". the parser in the
> mdfplugin would flag this as a parser error and do some other
> crazy stuff in other places. i've corrected the plugin to handle
> this situation more generously and consistently.
>
>> 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
>
> looking at the change log for the mdfplugin, it looks as if its
> functionality has not been significantly changed since may 2004.
>
> there is still one problem interfering with a nice visualization
> and that is impossible to solve with any method: your system has
> bonds across periodic images. While that is treated correctly in
> LAMMPS, VMD will always display them as bonds within the same
> periodic image. thus it may be better to use some other representation
> for that part of the model.
>
> check out the attached pair of "good" and "bad" examples.
>
> [...]
>
> cheers,
> axel.
>
>>
>> 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.
> <bad-viz.gif><nice-viz.gif>