[gmx-users] principal component analysis

[yoshizawa006 at yahoo.co.jp]

Dear David, 
thank you very much for your reply! 
Indeed I have used -type dihedral. 
Could it be, the problem lies in the [].tpr and [].xtc files? I mean, which subset of atoms must I choose in those files? (This very part of the previous discussion was obscure to me!) 
Best wishes! 
Maki Yoshizawa 
 
 David van der Spoel <spoel at xray.bmc.uu.se> wrote: yoshizawa006 at yahoo.co.jp wrote:
> Hello,
> 
> I would like to use PCA analysis in the dihedral space.
> 
> Despite having read the topics related to this issue in the GROMACS page 
> I am not quite sure how to accomplish this :-)
> 
> The -or option in the g_angle (version 3.3) seems not to be working. I 
> am already using an index file as sugested in the archives.
more info please.
did you use -type dihedral ?

> 
> Best wishes 
> 
> Maki Yoshizawa
> 
> 
> 
> 
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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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