[gmx-users] PCA average structure

[nadiav at soton.ac.uk]

Hi,

Thank you for your reply.

Regards,

Nadia Vahdati


Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> nadiav at soton.ac.uk wrote:
> > Hi gromacs users,
> >
> > Recently I asked about running PCA on MD output from Amber which was
> > helpful.    Based on the advise I used g_covar to run PCA on all atoms.
> > When I look at my average structure or filtered trajectory, I notice
> that
> > some of the bonds are much shorter than expected, and in the case of
> NH3 or
> > Hydrogens bound to C or N the bonds are even shorter, making the H's on
> the
> > NH3 group to ready bunch up together.
> >
> > for example for Lysine the bond between CD and CE are reduced from 1.53
> > Angstroms to 0.79 and for CE to HE2 from 1.00 to 0.49 and for NZ to HZ2
> in
> > the NH3, from 1.00 to 0.28
> >
> > Is the average structure a true Cartesian average?
> >
> yes, therefore you can expect it to be non-physical.
>
>
> > Thank you in advance.
> >
> > Nadia Vahdati
> >
> > J.W.Essex group
> > University of Southampton
> > UK.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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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://folding.bmc.uu.se
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