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

[mark.abraham at anu.edu.au]

So we're expecting a histogram of an all-against-all RMSD calculation over 3000-odd elements. So we should expect that around 3000*3000*0.5 entries exist in the histogram... that's about 4500000 entries. That sounds familiar, now :-) For 3002 elements, excluding self-comparisons, there are 3001-choose-2 combinations, i.e. 3001*3000*0.5, which is the number you give below. The values in this column are consistent with a histogram.

Mark

----- Original Message -----
From: OZGE ENGIN <OZENGIN at KU.EDU.TR>
Date: Friday, February 15, 2008 6:32 pm
Subject: Re: Re: Re: [gmx-users] still got the problem with the output of g_cluster
To: gmx-users at gromacs.org
Cc: gmx-users at gromacs.org

> 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
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