[gmx-users] PCA average structure
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 9 19:32:47 CEST 2006
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
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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://folding.bmc.uu.se
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