VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 12 2010 - 13:11:32 CST

hello benjamin,

On Tue, Jan 12, 2010 at 12:04 PM, Benjamin Bouvier
<benjamin.bouvier_at_ibcp.fr> wrote:
> Hello list,
>
> I'm having trouble getting Axel's HOOMD plugin (from
> http://sites.google.com/site/akohlmey/software/hoomd-plugin) to work with
> VMD 1.8.7 (on 32-bit Linux, obtained as a binary from the VMD site).
>
> Compilation went through with a couple of 'unused parameter' warnings. I
> copied the resulting hoomdplugin.so file to the
> $VMDBASEDIR/plugins/LINUX/molfile directory. To be on the safe side I also
> copied the headers to $VMDBASEDIR/plugins/include (molfile_plugin.h and

this is pointless and serves not purpose. the header is only used for
compilation
of the plugin and not an exported API.

> vmdplugin.h were already there). 'puts $auto_path' from VMD seems to points
> to the correct directory structure.
>
> Yet I cannot seem to find any HOOMD-XML entry in the load/save format
> pull-downs.

i suggest you start vmd in text mode and then check the startup message for
a line new plugin(s) being found. if it doesn't show up, you may have some
incompatibility between the VMD runtime libraries and what you compiled
the plugin against. another possible problem could be due to SELinux. there
may be some problems loading DSOs into programs in enforcing mode.
there are some magical incantations needed to override this (or you can
just disable SELinux).

> The approach suggested on the HOOMD site, e. g.:
>  package require topotools 1.0
>  animate write hoomd file.xml waitfor all

well, that will only work if the plugin is loaded.

> does not work either (Unknown coordinate file type hoomd)
>
> What am I missing? How can I check that the plugin is loaded OK?

see above. there also is the "plugin" command.
try: plugin list

cheers,
    axel.

>
> Thanks,
>
> --
> Benjamin
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.