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<P>Dear David,
<P>thank you very much for your reply!
<P>Indeed I have used -type dihedral.
<P>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!)
<P>Best wishes!
<P>Maki Yoshizawa
<P>
<P> <B><I>David van der Spoel <spoel@xray.bmc.uu.se></I></B> wrote:
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">yoshizawa006@yahoo.co.jp wrote:<BR>
> Hello,<BR>
> <BR>
> I would like to use PCA analysis in the dihedral space.<BR>
> <BR>
> Despite having read the topics related to this issue in the GROMACS page <BR>
> I am not quite sure how to accomplish this :-)<BR>
> <BR>
> The -or option in the g_angle (version 3.3) seems not to be working. I <BR>
> am already using an index file as sugested in the archives.<BR>
more info please.<BR>
did you use -type dihedral ?<BR>
<BR>
> <BR>
> Best wishes <BR>
> <BR>
> Maki Yoshizawa<BR>
> <BR>
> <BR>
> <BR>
> <BR>
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<BR>
<BR>
-- <BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>
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