[gmx-users] Re: dPCA

David spoel at xray.bmc.uu.se
Thu Oct 13 22:03:01 CEST 2005

On Thu, 2005-10-13 at 11:48 -0700, Gia Maisuradze wrote:
> Dear David,
> I have checked the changes in new Gromacs 3.3. It says that dihedral
> PCA is supported in g_angle (you are the author). Does it mean that we
> can do dihedral principal component analysis for proteins? Is it the
> same type of analysis that has been done by Gerhard Stock' group
> (PROTEINS, 58, 45, 2005)? If yes, I don't clearly understand how I can
> do that. Normal PCA (in cartesian coordinates) can be done by using
> g_covar, where we build the covariance matrix and diagonalize it, and
> get eigenvectors and eigenvalues. Then analyze them.
> Could you, please, explain how I can do dPCA on Gromacs, if it is
> possible.
Yes, you use g_angle -oc to produce a new trajectory file containing:
cos(phi) sin(phi) cos(psi) sin(psi) etc.
This you run through g_covar.

According to some people this information is not really useful for
protein analysis, as it can show many false minima and it is hard to go
back to real space. Barriers you see may be trivial due to overlapping

> The same question I have asked Erik Lindahl, but he did not know about
> dPCA in new Gromacs version.
> Thanks,
> Gia    
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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