[gmx-users] the DNA md simulation

rajendra kumar rjdkmr at gmail.com
Sat Feb 4 11:37:52 CET 2012

On Sat, Feb 4, 2012 at 8:27 AM, Banafsheh Mehrazma <bmehrazma at gmail.com>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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