[gmx-users] g_covar

[Tsjerk Wassenaar]

Hi Anthony,

Actually it shouldn't really matter, as long as the fit is consistent
(each frame least squares fitted to the same structure). However, if
you say average structure, do you mean the average structure before a
fit or after a fit? I hope you'll mean the last, since the second
makes no sense, really. So fitting to that average is actually the
same as fitting every frame to the reference (first frame) you used
for fitting in the first place.

I hope this clears things up a bit,

Tsjerk


On 8/19/05, David <spoel at xray.bmc.uu.se> wrote:
> On Fri, 2005-08-19 at 12:55 -0600, Anthony Cruz wrote:
> > Hi users:
> > I have a question about g_covar for essential dynamics.  What structure I
> > better use to fit, the average or the first structure of the trajectory?
> > Because the result will change depending in this selection.
> It's probably better to use the average. We'll probably try to implement
> another method that doesn't require superposition.
> >
> > 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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