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

Berk Hess gmx3 at hotmail.com
Mon Mar 12 13:40:56 CET 2007

>From: Alexandra Patriksson <alexandra at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] g_sham -dim ? (fwd)
>Date: Mon, 12 Mar 2007 12:39:54 +0100 (CET)
>  Alexandra Patriksson, PhD student
>  Molecular Biophysics program,
>  Dept. of Cell & Molecular Biology
>  Uppsala University
>---------- 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.


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