[gmx-users] essential dynamics

David spoel at xray.bmc.uu.se
Tue Aug 9 08:23:32 CEST 2005

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 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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