[gmx-users] g_sham -dim ? (fwd)

[David van der Spoel]

>> ---------- Forwarded message ----------
>> Date: Mon, 12 Mar 2007 11:40:54 +0100 (CET)
>> From: Alexandra Patriksson <alexandra at xray.bmc.uu.se>
>> To: gmx_users at gromacs.org
>> Subject: g_sham -dim ?
>>
>>
>> I would like to do a 3D-histogramanalysis using three principal 
>> components derived from a PCA analysis using all coordinates of a 
>> protein trajectory, but is a bit confused about the -dim flag. If I 
>> use -dim 3 3 3 (because of distances in three dimensions) I either get 
>> Ptot = Inf or Fatal error, depending on which version of the program I 
>> use. My question is - should I use this -dim flag at all or can I keep 
>> it at the default value of 1 1 1 ?
> 
> Each principal component is a single dimension, not a distance
> between two particles in 3D space.
> Therefore you should use 1 1 1.
> 
> Berk.
> 
But isn't a principal component a distance from a point (the average)?

-- 
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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