From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Sat Aug 21 2010 - 15:58:24 CDT
I have a couple of questions for people with long experience using NAMD and have publishing experience
I ran some simulations so as to see unfolding, but the molecule didn't really unfold, so I ran production at 500 and this is when some residues developed alpha helix that s absent in the native structure. My colleague suggested that CHARMM stabilizes the alpha helix, but I tried to google that and didn't get any useful hits to confirm that. So does anyone know if this is the case and have papers stating that?
Also I was wondering if in case one published that, readers would wonder why another software was used for comparison.
Your feedback is highly appreciated! Thanks!
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