[gmx-users] PCA average structure

nadiav at soton.ac.uk nadiav at soton.ac.uk
Mon Oct 9 19:25:57 CEST 2006

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?

Thank you in advance.

Nadia Vahdati

J.W.Essex group
University of Southampton

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