[gmx-users] still got the problem with the output of g_cluster

Thu Feb 14 23:46:03 CET 2008

Hi Mark,

You are right. While I am writing,most of the things in my mind are lost :)

The actual command line is:

g_cluster -s .tpr -f .xtc -dist 

and it gives a output file named rmsd-dist.xvg. In the first column, the rmsd values are written. However, I can not understand the values in the second column, the title of second column is only indicated. No explanation has been made in the manual. 

The frame number is 3000. One of the numbers on that column exceeds that value.

-----Original Message-----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Fri, 15 Feb 2008 09:11:55 +1100
Subject: Re: [gmx-users] still got the problem with the output of g_cluster

> Hi all,
> I have still got the problem with the second column of the output of g_cluster with -dist option. Xavier said that the a.u stands for arbitrary unit and I think it gives the histogram of rmsd value distribution. If so, I can not understand why the total of this column is not equal to the total number of conformations obtained from the simulation.

Well, what is it equal to? How many frames are you using, what are your 
actual command lines? Can you provide a short excerpt of the .xvg file?

Please consider the point of view of the people of whom you're asking 
such a question. Unless they're actually fluent with the code and useage 
of g_cluster, they don't have the answer at their fingertips. However if 
you give them useful information, they might be able to see things that 
you can't. If you don't provide useful information, then even users who 
do have the answer at their fingertips might decide you're not worth 
their time :-)

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Ozge Engin
Computational Science & Engineering
Koc University

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