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

[OZGE ENGIN]

Sorry Mark, the sum of the 2 nd column is 4501500. The frame number is 3002.


-----Original Message-----
From: mark.abraham at anu.edu.au
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Fri, 15 Feb 2008 10:04:45 +1100
Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster

What's the sum of the second column?

Mark

----- Original Message -----
From: OZGE ENGIN <OZENGIN at KU.EDU.TR>
Date: Friday, February 15, 2008 9:46 am
Subject: Re: Re: [gmx-users] still got the problem with the output of g_cluster
To: gmx-users at gromacs.org

> 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
> 
> OZGE ENGIN wrote:
> > 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 :-)
> 
> Mark
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> 
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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Ozge Engin
=================================
Computational Science & Engineering
Koc University