[gmx-users] essential dynamics

[David]

On Wed, 2005-08-10 at 07:13 -0600, Anthony Cruz wrote:
> Thank you for your answer.
> 
> The other question is when I do the cosen content analysis I suppose to use 
> the principal components that have the lower conten??
I think so, but please read the paper
Hess, Phys. Rev. E. 65, 031910 (2002)
> 
> Thanks Anthony
> 
> On Tuesday 09 August 2005 12:23 am, David wrote:
> > On Mon, 2005-08-08 at 16:45 -0600, Anthony Cruz wrote:
> > > Hi Users:
> > > I am interested in perform essential dynamics analysis to my simulation
> > > and I have some questions.
> > > For the analysis I will use the part of the trajectory when the rmsd is
> > > constant or all the trajectory?
> >
> > Assuming you have an equilibrium trajectory you should use all. If you
> > only want to study what happens very close to the crystal structure you
> > could use a subset, but how do you justify that?
> >
> > > When I do the Posen cosen analysis, I will use the PC's that have the
> > > lower values?
> >
> > Don't understand the question.
> >
> > > Thanks
> > > Anthony
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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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