From: Axel Kohlmeyer (
Date: Mon Aug 06 2007 - 11:29:16 CDT

On Mon, 6 Aug 2007, Audrey Salazar wrote:

dear audrey,

let me congratulate you for giving an excellent
example of how e-mails to mailing lists asking for
help should be written. i wish more people would
put in this effort, as it makes it _so_ much easier
to respond in a concise way. thanks.

i guess that peter will address your specific problems
in more detail (he is the expert), but you may want
to have a look at the autopsf plugin documentation at:
and particularly:

also, if you see a way to augment the documentation to make
it easier to understand for people new to using the plugin,
we would appreciate it a lot (this is the thing that is usually
is the hardest to do).

thanks again and good luck with your simulations,

AS> Dear VMD-L,

AS> I am a first year graduate student studying nucleic acids using the
AS> all27 force field in NAMD. At present, I am interested in making a
AS> short, single stranded RNA solvated with water molecules in VMD.
AS> Below, I outline my procedure intermingled with questions, highlighted
AS> by the **. I would appreciate any help that the VMD community might
AS> be able to provide.


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.