[lammps-users] For Axel: Triclinic cell support in VMD

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1

Axel,

I was searching through the mailing list, and saw you had implemented triclinic cell support in VMD.
I would be interested in getting a copy of the source code for this, for some of the things I am currently working on. You said you would be able to supply this for users to compile themselves.

Thank you,
Michael Doig

2

michael,

the easiest way to get access to the new code is
to download and install the latest VMD alpha binaries.

http://www.ks.uiuc.edu/Research/vmd/alpha/
this page tells you how to access them.

they'll also have the topotools plugins with triclinic
cell read support included.

i'll try to put together a small package to compile
a standalone molfile plugin. and will attach it to

http://sites.google.com/site/akohlmey/software/lammps-icms

axel.

3

Axel,

Do I need to do anything else after installing the latest alpha version of VMD?
I installed V. 1.8.8a18, and tried to read a LAMMPS trajectory file which has a triclinic cell, and VMD just crashes with the error below:

My simulation itself runs ok, because I can visualise xyz coordinates if I dump them.

Does the alpha version contain the updated lammpsplugin, or was that the molfile plugin you were referring to, and will I need that to get it to work.

Regards,
Michael

4

michael,

Axel,

Do I need to do anything else after installing the latest alpha version
of VMD?

not really.

I installed V. 1.8.8a18, and tried to read a LAMMPS trajectory file
which has a triclinic cell, and VMD just crashes with the error below:

that is strange. that error message should only appear
in an older version of VMD. can you make a test file available?

My simulation itself runs ok, because I can visualise xyz coordinates if
I dump them.

Does the alpha version contain the updated lammpsplugin, or was that the
molfile plugin you were referring to, and will I need that to get it to
work.

the VMD development cvs has all updates. i have uploaded the sources
here as well. just unpack, type make (assuming that you are running linux)
and copy the lammpsplugin.so file over the existing one in your
VMD-1.8.7 installation. if you launch vmd, you should then see a message
that there is one new plugin.

http://sites.google.com/site/akohlmey/software/lammps-icms/vmd-lammpsplugin-20100810.tar.gz?attredirects=0&d=1

axel.

5

Thanks Axel, that works great now.

Regards,
Michael.