[gmx-users] RMSD

[David van der Spoel]

Dhananjay wrote:
> 
> The starting structure is a homology model. 
> (If you need some more details then please tell me)

well that explains it probably, the starting structure is not a good 
protein structure. you can use the MD to tell you why the model falls apart.

> 
> force field :  GROMOS96 43a1


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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