[gmx-users] the 2 nd column of the output of g_cluster with -dist option

[OZGE ENGIN]

Xavier,

The output file of g_cluster with -dist option then gives the histogram of rmsd value distribution, is it?
If it is the case, after plotting these data,I observe that the distribution resembles a gaussian type, its mean is located around 0.4 nm. This value is bigger compared to yours. Is it feasible? 
I performed my remd simulation in vacuum. It may be the reason?

-----Original Message-----
From: "Xavier Periole" <X.Periole at rug.nl>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 12 Feb 2008 23:10:02 +0100
Subject: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist	option

On Tue, 12 Feb 2008 23:55:35 +0200
  "OZGE ENGIN" <OZENGIN at KU.EDU.TR> wrote:
> Hi all, 
> 
> What does the second column of the output file of g_cluster with -dist 
>option stand for? Its title is a.u. I think it is atomic unit? In the manual, 
>it is not described.

I believe a.u. stands for arbitrary unit. It should be the normalized
distribution. You can check by integrating the curve ... should be one.

XAvier

> 
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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Ozge Engin
=================================
Computational Science & Engineering
Koc University