[gmx-users] essential dynamics

[David van der Spoel]

On Fri, 2004-09-24 at 14:56, Isabella Daidone wrote:
> Sorry if I'm not right,
> but using g_covar with the option -ref should provide what smith is 
> asking for.
> Is it correct?
> 
It seems like you are right, I didn't know this option existed. Sorry
for the confusion!
> Ciao
> Isabella
> 
> On Fri, 24 Sep 2004, David van der Spoel wrote:
> 
> > 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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> >
> _______________________________________________
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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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