From: Axel Kohlmeyer (
Date: Fri Jun 26 2009 - 07:09:06 CDT

On Fri, 2009-06-26 at 10:48 +0200, Bjoern Olausson wrote:
> Hi all,

hi bjoern,

> I am just curious about the analytical capabilities of VMD. So far I used
> CHARMM to setup, run and analyze my simulations. Now I setup and analyze my
> simulations with CHARMM but run them with NAMD.
> There are some deficiencies in the CHARMM programming language which drive me
> crazy ;) (I am accustomed to the flexible and charming python language)

> So now my questions might be a bit generic, but is VMD (with TCL in mind)
> capable of doing all sort of evaluation one can do with CHARMM?

i don't know CHARMM that well, but there is a lot you can do with VMD.
in total i would expect that VMD is better for doing some operations
and worse for others. the main difference is that VMD is deliberately
very agnostic about the data you feed it. on the other hand, missing
capability can be augmented through customized scripting and writing
plugins, if you are not afraid of programming.

> Are there any limitations or tasks you are aware, one could not use VMD/TCL
> Especially mathematical operations like vectors, time-series, and so on...

VMD has all the mathematical operations the embedded script languages
provide (there is tcl _and_ a python interpreter) and then some
customized helpers. don't expect the flexibility of maple, mathematica
or matlab. i would also say that it is a mistake to try and use VMD
"the CHARMM way", as there also is a "VMD-way" of doing things, i.e.
it may take a little while to get used to that execution and data

> I know this is a very generic question, but I would like to know a bit more
> before I throw myself into TCL and then realize that I face questions I can't
> cope with VMD/TCL and see myself creeping back to CHARMM ;-)

the best you can do to inform yourself, is to read through the script
interface part of the VMD user's guide and have a look at the VMD
tutorials (and the tcl tutorial bundled with tcl 8.5 or on

as far as the python interface goes, you should keep in mind that this
is not complete and doesn't have many support packages, but as of the
latest VMD 1.8.7 beta versions you can call tcl from python (calling
python from tcl exists a bit longer)

> Ah, one more thing: Can I run VMD/TCL headless on a compute node?



> Thanks in advance
> kind regards
> Bjoern

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.