[gmx-users] essential dynamics

[David van der Spoel]

On Fri, 2004-09-24 at 14:12, smith wrote:
>   dear users,
> 
> 
> 
> 
> 
> 
> 
> Can essential dynamcis be perfomed in gromacs chosing the reference as starting structure rather than average one.
> 
Not really, since the covariance analysis actually analyzes the variance
around the average. What you may want to do is to look at the 2d
projection plots and project the starting structure on it as well, such
that you can see whether or not you are sampling close to the starting
structure.
> thanks for any help
> 
> smith
> 
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-- 
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://xray.bmc.uu.se/~spoel
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