From: Peter Freddolino (
Date: Fri Jan 20 2006 - 09:06:49 CST

Hi Lavina,
this is going to depend greatly on exactly what you'd like to do. When
you say you'd like to create a demo, do you mean you want something to
show other people, or something to help you learn? There are a few
additional tutorials available from the KS website that get into more
detailed applications, for example the Gramidicin tutorial
( and
nanotube tutorial
( Beyond that, you
are going to be getting in to real research level work, and thus you
should read some recent MD papers to figure out what is being done in
the field, and apply similar techniques to a protein of your choice.

Could you be more specific on what kind of problems you are having with
the avidin-biotin simulation? Depending on their nature, you may want to
try the NAMD mailing list as well.


Lin wrote:

>I am doing an university project in 3d biological
>simulation. I am a newbie in MD and i have went through
>the VMD and NAMD tutorials and created some simple
>simulations. However, i wish to try more complicated
>cases and I found the avidin-biotin simulation in the VMD
>website and hence would like to try. however, I have
>problem getting the results as mentioned in the paper I
>have found as I have very limited knowledge in the area.
>Does anyone have any idea what would be a suitable
>that a novice can try creating for a demo? I have tried
>exploring the different parameters/options for applying
>SMD to alanin and moving them ard, however I need to do
>something that is biologically and chemically correct.
>Thank you and I look forward to replies!!
>Best Regards,
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