On Sat, Feb 4, 2012 at 8:27 AM, Banafsheh Mehrazma <[email protected]>wrote:
> Dear Justin; > I specified the terminal residues in the *.mdp file, just like what in > my force field has (DNA.rtp) mentioned. I wonder if we should some > thing else with it? I mean, when I viewed my molecule with VMD, after > a 5 ns simulation, my terminal residues were not in front of each > other, they are slanted inward the helix. > I don't know, whether it is right or not! > > Best regards > B.Mehrazma > > Which force field you are using? If terminal base pair is A-T then it would not much stable during the simulation while C-G would be more stable. Base pair parameters could fluctuate during simulations. With Regards, Rajendra Kumar Max-Planck-Institut fuer biophysikalische Chemie Dep. of Theoretical and computational Biophysics, Am Fassberg 11, 37077 Goettingen, Germany Tel.: +49 551 201 2304 Website: http://www.mpibpc.mpg.de/home/grubmueller/index.html
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