[EMAIL PROTECTED] 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 <[EMAIL PROTECTED]>/* wrote:
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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