[gmx-users] principal component analysis

[David van der Spoel]

yoshizawa006 at yahoo.co.jp wrote:
> 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!)

for the g_angle analysis you need the normal tpr file.
for the g_covar you need a dummy tpr file with 2n/3 atoms where n is the 
  number of dihedrals you want to analyze.

> 
> 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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-- 
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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