VMD-L Mailing List

From: Lin (lavizgal_at_yahoo.com.sg)
Date: Wed Jan 18 2006 - 23:31:06 CST

Hi,

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
simulation
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,
Lavina

                
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