Hello all,
I'm trying to reproduce self diffusion coefficients from NMR for two
disaccharides in explicit waters using a similar procedure to that outlined
in
Corzana, F. et al. J. Comput. Chem. 2004, v 25, 4, pp 573-586
The authors obtained the self-diffusion coefficients computationally "via
the Stokes-Einstein relation and the center of mass mean-square displacement
autocorrelation". I'm first trying to reproduce the results from this
publication to establish the method before looking at other sugars. I've
tried using the "diffusion" function in ptraj but my results are
inconsistent (off by an order of magnitude). Am I trying to obtain this
value correctly?
Matthew Tessier
mbt3911.uga.edu
matthew.tessier.gmail.com
Woods' Lab Room 2069
Complex Carbohydrate Research Center - University of Georgia
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 21 2010 - 11:30:02 PDT
